Note that there are currently many imported or generated files with trailing spaces: files for building on Windows and macOS (*.wixproj, *.wxs, *.icns, *.nib, etc), test data files (for xml, email, etc), sources of third-party libraries (libffi, blake2), etc.
Try to run

git ls-tree -r main --name-only | tr '\n' '\0' | xargs -0 sed -ri -e 's/ +$//'

and then

git diff --stat

to get a list of files containing trailing spaces.

In this case I can move this directive to only address .py, .c, .h, .rst, .md, .yml. What do you think?

By the way, shouldn't make patchcheck complain about this trailing whitespace?

Running the suggested sed and then aggregating data by file extension it looks like this:

  40 wxs
  20 wixproj
  14 c
  11 h
   9 icns
   7 xml
   6 pem
   6 ico
   4 txt
   4 rtf
   4 png
   4 TXT
   3 rc
   3 py
   3 html
   3 S
   2 wav
   2 targets
   2 au
   2 aiff
   2 2
   1 xbm
   1 wxl
   1 thm
   1 sample
   1 pyobjc
   1 psd
   1 ps
   1 pdf
   1 patch
   1 md
   1 lproj/PreferenceWindow
   1 lproj/MyDocument
   1 lproj/MainMenu
   1 github/problem-matchers/sphinx
   1 github/SECURITY
   1 def
   1 cpp
   1 app/Contents/Resources/IDLE
   1 Modules/_ctypes/libffi_osx/README
   1 Modules/_ctypes/darwin/README
   1 Modules/_ctypes/darwin/LICENSE
   1 Lib/distutils/command/command_template
   1 4
   1 3

So yeah, I do think that limiting whitespace trimming to the extensions I highlighted above will do the job.

LGTM. And maybe exclude some directories like Modules/_blake2/impl/, Modules/_ctypes/libffi_osx/, etc? I am not sure what is the status of these files and how they are supposed to be synchronized with upstream.

As for patcheck, it is just not used for C files.