diff --git a/docs/changelog/3235.bugfix.rst b/docs/changelog/3235.bugfix.rst
new file mode 100644
index 000000000..cbd369baa
--- /dev/null
+++ b/docs/changelog/3235.bugfix.rst
@@ -0,0 +1,2 @@
+Fix crash with fresh subprocess, if the build backend is setuptools automatically enable fresh subprocesses for
+build backend calls - by :user:`gaborbernat`.
diff --git a/docs/config.rst b/docs/config.rst
index a52358f6d..351190a1a 100644
--- a/docs/config.rst
+++ b/docs/config.rst
@@ -797,7 +797,7 @@ Python virtual environment packaging
 .. conf::
    :keys: fresh_subprocess
    :version_added: 4.14.0
-   :default: False
+   :default: True if build backend is setuptools otherwise False
 
    A flag controlling if each call to the build backend should be done in a fresh subprocess or not (especially older
    build backends such as ``setuptools`` might require this to discover newly provisioned dependencies).
diff --git a/src/tox/config/main.py b/src/tox/config/main.py
index a073911bb..a409aaa0a 100644
--- a/src/tox/config/main.py
+++ b/src/tox/config/main.py
@@ -40,7 +40,7 @@ def __init__(  # noqa: PLR0913
             self._overrides[override.namespace].append(override)
 
         self._src = config_source
-        self._key_to_conf_set: dict[tuple[str, str], ConfigSet] = OrderedDict()
+        self._key_to_conf_set: dict[tuple[str, str, str], ConfigSet] = OrderedDict()
         self._core_set: CoreConfigSet | None = None
         self.memory_seed_loaders: defaultdict[str, list[MemoryLoader]] = defaultdict(list)
 
@@ -131,7 +131,7 @@ def get_section_config(  # noqa: PLR0913
         for_env: str | None,
         loaders: Sequence[Loader[Any]] | None = None,
     ) -> T:
-        key = section.key, for_env or ""
+        key = section.key, for_env or "", "-".join(base or [])
         try:
             return self._key_to_conf_set[key]  # type: ignore[return-value] # expected T but found ConfigSet
         except KeyError:
@@ -154,7 +154,7 @@ def get_env(
         """
         Return the configuration for a given tox environment (will create if not exist yet).
 
-        :param item: the name of the environment
+        :param item: the name of the environment is
         :param package: a flag indicating if the environment is of type packaging or not (only used for creation)
         :param loaders: loaders to use for this configuration (only used for creation)
         :return: the tox environments config
@@ -170,7 +170,7 @@ def get_env(
 
     def clear_env(self, name: str) -> None:
         section, _, __ = self._src.get_tox_env_section(name)
-        del self._key_to_conf_set[(section.key, name)]
+        self._key_to_conf_set = {k: v for k, v in self._key_to_conf_set.items() if k[0] == section.key and k[1] == name}
 
 
 ___all__ = [
diff --git a/src/tox/config/of_type.py b/src/tox/config/of_type.py
index 99d3d19dd..a53456c82 100644
--- a/src/tox/config/of_type.py
+++ b/src/tox/config/of_type.py
@@ -58,6 +58,10 @@ def __call__(
     def __eq__(self, o: object) -> bool:
         return type(self) == type(o) and super().__eq__(o) and self.value == o.value  # type: ignore[attr-defined]
 
+    def __repr__(self) -> str:
+        values = ((k, v) for k, v in vars(self).items() if v is not None)
+        return f"{type(self).__name__}({', '.join(f'{k}={v}' for k, v in values)})"
+
 
 _PLACE_HOLDER = object()
 
@@ -111,7 +115,7 @@ def __call__(
         return cast(T, self._cache)
 
     def __repr__(self) -> str:
-        values = ((k, v) for k, v in vars(self).items() if k != "post_process" and v is not None)
+        values = ((k, v) for k, v in vars(self).items() if k not in {"post_process", "_cache"} and v is not None)
         return f"{type(self).__name__}({', '.join(f'{k}={v}' for k, v in values)})"
 
     def __eq__(self, o: object) -> bool:
diff --git a/src/tox/config/sets.py b/src/tox/config/sets.py
index d15a59134..ebb46be69 100644
--- a/src/tox/config/sets.py
+++ b/src/tox/config/sets.py
@@ -94,19 +94,17 @@ def _add_conf(self, keys: Sequence[str], definition: ConfigDefinition[V]) -> Con
         key = keys[0]
         if key in self._defined:
             self._on_duplicate_conf(key, definition)
-        else:
-            self._keys[key] = None
-            for item in keys:
-                self._alias[item] = key
-            for key in keys:
-                self._defined[key] = definition
+
+        self._keys[key] = None
+        for item in keys:
+            self._alias[item] = key
+        for key in keys:
+            self._defined[key] = definition
         return definition
 
     def _on_duplicate_conf(self, key: str, definition: ConfigDefinition[V]) -> None:
-        earlier = self._defined[key]
-        if definition != earlier:  # pragma: no branch
-            msg = f"config {key} already defined"
-            raise ValueError(msg)
+        msg = f"duplicate configuration definition for {self.name}:\nhas: {self._defined[key]}\nnew: {definition}"
+        raise ValueError(msg)
 
     def __getitem__(self, item: str) -> Any:
         """
diff --git a/src/tox/execute/pep517_backend.py b/src/tox/execute/pep517_backend.py
index 06032ba24..8d8bf8e91 100644
--- a/src/tox/execute/pep517_backend.py
+++ b/src/tox/execute/pep517_backend.py
@@ -91,6 +91,7 @@ def close(self) -> None:
                     execute.process.wait(timeout=0.1)  # pragma: no cover
                 except TimeoutExpired:  # pragma: no cover
                     execute.process.terminate()  # pragma: no cover  # if does not stop on its own kill it
+            self._local_execute = None
         self.is_alive = False
 
 
diff --git a/src/tox/session/env_select.py b/src/tox/session/env_select.py
index 9d6c25c2f..4d5327eed 100644
--- a/src/tox/session/env_select.py
+++ b/src/tox/session/env_select.py
@@ -239,12 +239,12 @@ def _env_name_to_active(self) -> dict[str, bool]:
     def _defined_envs(self) -> dict[str, _ToxEnvInfo]:  # noqa: C901, PLR0912
         # The problem of classifying run/package environments:
         # There can be two type of tox environments: run or package. Given a tox environment name there's no easy way to
-        # find out which it is.  Intuitively a run environment is any environment that's not used for packaging by
-        # another run environment. To find out what are the packaging environments for a run environment you have to
-        # first construct it. This implies a two phase solution: construct all environments and query their packaging
-        # environments. The run environments are the ones not marked as of packaging type. This requires being able
-        # to change tox environments type, if it was earlier discovered as a run environment and is marked as packaging
-        # we need to redefine it, e.g. when it shows up in config as [testenv:.package] and afterwards by a run env is
+        # find out which it is.  Intuitively, a run environment is any environment not used for packaging by another run
+        # environment. To find out what are the packaging environments for a run environment, you have to first
+        # construct it. This implies a two-phase solution: construct all environments and query their packaging
+        # environments. The run environments are the ones not marked as of packaging type. This requires being able to
+        # change tox environments types, if it was earlier discovered as a run environment and is marked as packaging,
+        # we need to redefine it. E.g., when it shows up in config as [testenv:.package] and afterward by a run env is
         # marked as package_env.
 
         if self._defined_envs_ is None:  # noqa: PLR1702
@@ -267,7 +267,7 @@ def _defined_envs(self) -> dict[str, _ToxEnvInfo]:  # noqa: C901, PLR0912
                     try:
                         run_env.package_env = self._build_pkg_env(pkg_name_type, name, env_name_to_active)
                     except Exception as exception:  # noqa: BLE001
-                        # if it's not a run environment,  wait to see if ends up being a packaging one -> rollback
+                        # if it's not a run environment, wait to see if ends up being a packaging one -> rollback
                         failed[name] = exception
                         for key in self._pkg_env_counter - start_package_env_use_counter:
                             del self._defined_envs_[key]
@@ -320,6 +320,7 @@ def _build_run_env(self, name: str) -> RunToxEnv | None:
         journal = self._journal.get_env_journal(name)
         args = ToxEnvCreateArgs(env_conf, self._state.conf.core, self._state.conf.options, journal, self._log_handler)
         run_env = runner(args)
+        run_env.register_config()
         self._manager.tox_add_env_config(env_conf, self._state)
         return run_env
 
@@ -363,6 +364,7 @@ def _get_package_env(self, packager: str, name: str, is_active: bool) -> Package
         journal = self._journal.get_env_journal(name)
         args = ToxEnvCreateArgs(pkg_conf, self._state.conf.core, self._state.conf.options, journal, self._log_handler)
         pkg_env: PackageToxEnv = package_type(args)
+        pkg_env.register_config()
         self._defined_envs_[name] = _ToxEnvInfo(pkg_env, is_active)
         self._manager.tox_add_env_config(pkg_conf, self._state)
         return pkg_env
diff --git a/src/tox/tox_env/api.py b/src/tox/tox_env/api.py
index 367209306..260252a68 100644
--- a/src/tox/tox_env/api.py
+++ b/src/tox/tox_env/api.py
@@ -68,8 +68,6 @@ def __init__(self, create_args: ToxEnvCreateArgs) -> None:
         self._interrupted = False
         self._log_id = 0
 
-        self.register_config()
-
     @property
     def cache(self) -> Info:
         return Info(self.env_dir)
diff --git a/src/tox/tox_env/python/virtual_env/package/pyproject.py b/src/tox/tox_env/python/virtual_env/package/pyproject.py
index 1b0aa5670..ef28a167e 100644
--- a/src/tox/tox_env/python/virtual_env/package/pyproject.py
+++ b/src/tox/tox_env/python/virtual_env/package/pyproject.py
@@ -107,8 +107,19 @@ def __init__(self, create_args: ToxEnvCreateArgs) -> None:
         self._package_dependencies: list[Requirement] | None = None
         self._package_name: str | None = None
         self._pkg_lock = RLock()  # can build only one package at a time
-        self.root = self.conf["package_root"]
         self._package_paths: set[Path] = set()
+        self._root: Path | None = None
+
+    @property
+    def root(self) -> Path:
+        if self._root is None:
+            self._root = self.conf["package_root"]
+        return self._root
+
+    @root.setter
+    def root(self, value: Path) -> None:
+        self._root = value
+        self._frontend_ = None  # force recreating the frontend with new root
 
     @staticmethod
     def id() -> str:
@@ -117,8 +128,7 @@ def id() -> str:
     @property
     def _frontend(self) -> Pep517VirtualEnvFrontend:
         if self._frontend_ is None:
-            fresh = cast(bool, self.conf["fresh_subprocess"])
-            self._frontend_ = Pep517VirtualEnvFrontend(self.root, self, fresh_subprocess=fresh)
+            self._frontend_ = Pep517VirtualEnvFrontend(self.root, self)
         return self._frontend_
 
     def register_config(self) -> None:
@@ -140,7 +150,7 @@ def register_config(self) -> None:
         self.conf.add_config(
             keys=["fresh_subprocess"],
             of_type=bool,
-            default=False,
+            default=self._frontend.backend.split(".")[0] == "setuptools",
             desc="create a fresh subprocess for every backend request",
         )
 
@@ -377,10 +387,9 @@ def id() -> str:
 
 
 class Pep517VirtualEnvFrontend(Frontend):
-    def __init__(self, root: Path, env: Pep517VenvPackager, *, fresh_subprocess: bool) -> None:
+    def __init__(self, root: Path, env: Pep517VenvPackager) -> None:
         super().__init__(*Frontend.create_args_from_folder(root))
         self._tox_env = env
-        self._fresh_subprocess = fresh_subprocess
         self._backend_executor_: LocalSubProcessPep517Executor | None = None
         into: dict[str, Any] = {}
 
@@ -435,7 +444,7 @@ def _send_msg(
             if outcome is not None:  # pragma: no branch
                 outcome.assert_success()
         finally:
-            if self._fresh_subprocess:
+            if self._tox_env.conf["fresh_subprocess"]:
                 self.backend_executor.close()
 
     def _unexpected_response(  # noqa: PLR0913
diff --git a/tests/config/test_sets.py b/tests/config/test_sets.py
index f60c88673..c92eeeea2 100644
--- a/tests/config/test_sets.py
+++ b/tests/config/test_sets.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import re
 from collections import OrderedDict
 from pathlib import Path
 from typing import TYPE_CHECKING, Callable, Dict, Optional, Set, TypeVar
@@ -125,14 +126,24 @@ def test_config_dynamic_repr(conf_builder: ConfBuilder) -> None:
 def test_config_redefine_constant_fail(conf_builder: ConfBuilder) -> None:
     config_set = conf_builder("path = path")
     config_set.add_constant(keys="path", desc="desc", value="value")
-    with pytest.raises(ValueError, match="config path already defined"):
+    msg = (
+        "duplicate configuration definition for py39:\n"
+        "has: ConfigConstantDefinition(keys=('path',), desc=desc, value=value)\n"
+        "new: ConfigConstantDefinition(keys=('path',), desc=desc2, value=value)"
+    )
+    with pytest.raises(ValueError, match=re.escape(msg)):
         config_set.add_constant(keys="path", desc="desc2", value="value")
 
 
 def test_config_redefine_dynamic_fail(conf_builder: ConfBuilder) -> None:
     config_set = conf_builder("path = path")
     config_set.add_config(keys="path", of_type=str, default="default_1", desc="path")
-    with pytest.raises(ValueError, match="config path already defined"):
+    msg = (
+        "duplicate configuration definition for py39:\n"
+        "has: ConfigDynamicDefinition(keys=('path',), desc=path, of_type=<class 'str'>, default=default_1)\n"
+        "new: ConfigDynamicDefinition(keys=('path',), desc=path, of_type=<class 'str'>, default=default_2)"
+    )
+    with pytest.raises(ValueError, match=re.escape(msg)):
         config_set.add_config(keys="path", of_type=str, default="default_2", desc="path")
 
 
diff --git a/tests/session/cmd/test_sequential.py b/tests/session/cmd/test_sequential.py
index 92f6bd911..a8238008a 100644
--- a/tests/session/cmd/test_sequential.py
+++ b/tests/session/cmd/test_sequential.py
@@ -94,8 +94,7 @@ def test_result_json_sequential(
     assert "result" not in log_report["testenvs"][".pkg"]
 
     assert packaging_setup[-1][0] in {0, None}
-    assert packaging_setup[-1][1] == "_exit"
-    assert packaging_setup[:-1] == [
+    assert packaging_setup == [
         (0, "install_requires"),
         (None, "_optional_hooks"),
         (None, "get_requires_for_build_wheel"),
@@ -303,7 +302,6 @@ def test_skip_develop_mode(tox_project: ToxProjectCreator, demo_pkg_setuptools:
         (".pkg", "install_requires_for_build_editable"),
         (".pkg", "build_editable"),
         ("py", "install_package"),
-        (".pkg", "_exit"),
     ]
     assert calls == expected
 
diff --git a/tests/tox_env/python/virtual_env/package/test_package_cmd_builder.py b/tests/tox_env/python/virtual_env/package/test_package_cmd_builder.py
index 500e4e237..d29fe257c 100644
--- a/tests/tox_env/python/virtual_env/package/test_package_cmd_builder.py
+++ b/tests/tox_env/python/virtual_env/package/test_package_cmd_builder.py
@@ -71,7 +71,6 @@ def test_tox_install_pkg_sdist(tox_project: ToxProjectCreator, pkg_with_extras_p
         (".pkg_external_sdist_meta", "prepare_metadata_for_build_wheel", []),
         ("py", "install_package_deps", deps),
         ("py", "install_package", ["--force-reinstall", "--no-deps", str(pkg_with_extras_project_sdist)]),
-        (".pkg_external_sdist_meta", "_exit", []),
     ]
 
 
diff --git a/tests/tox_env/python/virtual_env/test_setuptools.py b/tests/tox_env/python/virtual_env/test_setuptools.py
index 5fe0acfaa..e99dba5c2 100644
--- a/tests/tox_env/python/virtual_env/test_setuptools.py
+++ b/tests/tox_env/python/virtual_env/test_setuptools.py
@@ -51,5 +51,5 @@ def test_setuptools_package(
     assert len(py_messages) == 5, "\n".join(py_messages)  # 1 install wheel + 3 command + 1 final report
 
     package_messages = [i for i in result if ".pkg: " in i]
-    # 1 optional hooks + 1 install requires + 1 build requires + 1 build meta + 1 build isolated + 1 exit
-    assert len(package_messages) == 6, "\n".join(package_messages)
+    # 1 optional hooks + 1 install requires + 1 build requires + 1 build meta + 1 build isolated
+    assert len(package_messages) == 5, "\n".join(package_messages)