I have a ~/.pydistutils.cfg with the following contents:

    [build_ext]
    force = true
    inplace = true

(--force is useful because sometimes just comparing timestamps is insufficient to know whether a package needs to be rebuilt, e.g. in the presence of external dependencies -- and I use ccache anyways to avoid paying for excessive rebuilds; --inplace is useful as I have quite a few packages with extension modules that are editably-installed).

With this ~/.pydistutils.cfg, cpython fails to build.  For example, having checked out v3.7.0 from a git clone (otherwise clean git repo, per `git clean -xfd`),

    mkdir build && cd build && ../configure && make

ultimately results in

    <elided>

    gcc -pthread -shared build/temp.linux-x86_64-3.7/home/antony/src/extern/cpython/Modules/_ctypes/_ctypes.o build/temp.linux-x86_64-3.7/home/antony/src/extern/cpython/Modules/_ctypes/callbacks.o build/temp.linux-x86_64-3.7/home/antony/src/extern/cpython/Modules/_ctypes/callproc.o build/temp.linux-x86_64-3.7/home/antony/src/extern/cpython/Modules/_ctypes/stgdict.o build/temp.linux-x86_64-3.7/home/antony/src/extern/cpython/Modules/_ctypes/cfield.o -L/usr/local/lib -lffi -ldl -o /home/antony/src/extern/cpython/build/_ctypes.cpython-37m-x86_64-linux-gnu.so
    *** WARNING: renaming "_struct" since importing it failed: build/lib.linux-x86_64-3.7/_struct.cpython-37m-x86_64-linux-gnu.so: cannot open shared object file: No such file or directory
    Traceback (most recent call last):
    File "../setup.py", line 442, in check_extension_import
        importlib._bootstrap._load(spec)
    File "<frozen importlib._bootstrap>", line 696, in _load
    File "<frozen importlib._bootstrap>", line 670, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 583, in module_from_spec
    File "<frozen importlib._bootstrap_external>", line 1043, in create_module
    File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
    ImportError: build/lib.linux-x86_64-3.7/_struct.cpython-37m-x86_64-linux-gnu.so: cannot open shared object file: No such file or directory

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
    File "../setup.py", line 2363, in <module>
        main()
    File "../setup.py", line 2358, in main
        "Tools/scripts/2to3", "Tools/scripts/pyvenv"]
    File "/home/antony/src/extern/cpython/Lib/distutils/core.py", line 148, in setup
        dist.run_commands()
    File "/home/antony/src/extern/cpython/Lib/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
    File "/home/antony/src/extern/cpython/Lib/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
    File "/home/antony/src/extern/cpython/Lib/distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
    File "/home/antony/src/extern/cpython/Lib/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
    File "/home/antony/src/extern/cpython/Lib/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
    File "/home/antony/src/extern/cpython/Lib/distutils/command/build_ext.py", line 339, in run
        self.build_extensions()
    File "../setup.py", line 308, in build_extensions
        self.check_extension_import(ext)
    File "../setup.py", line 447, in check_extension_import
        assert not self.inplace
    AssertionError
    make: *** [Makefile:618: sharedmods] Error 1

Removing the ~/.pydistutils.cfg fixes the issue and leads to a successful build.

I think(?) CPython's build system should essentially make sure that distutils behaves as if `--no-user-cfg` was in effect.  Or at least the limitation should be documented, but it's not very practical to have to temporarily rename an existing ~/.pydistutils.cfg whenever building CPython.  See also https://bugs.python.org/issue9309, perhaps.