Lib\sysconfig.py uses '{installed_base}/Include'
as the include directory on Windows, 

Lib\distutils\sysconfig.py uses 
elif os.name == "nt":
        return os.path.join(prefix, "include")

which is normally harmless because windows file systems
are case-preserving, but case-ignoring, but it leads to
a warning from pyinstaller:
https://github.com/pyinstaller/pyinstaller/issues/783

The directory referred to has a lowercase i (on my machine).

In my opinion both modules should use the spelling
that the installer uses when creating the directories.

Within the standard library, I think only the site module uses the top-level sysconfig module, which IIRC it uses to set up sys.path. 

Note that WINDOWS_SCHEME in distutils.command.install uses "Include". Also for virtual environments, venv.EnvBuilder.ensure_directories hard codes "Include".

Distutils is now deprecated (see PEP 632) and all tagged issues are being closed. From now until removal, only release blocking issues will be considered for distutils.

If this issue does not relate to distutils, please remove the component and reopen it. If you believe it still requires a fix, most likely the issue should be re-reported at https://github.com/pypa/setuptools