Hi!  Welcome to the joy of Python and thanks for the bug report and analysis.

> In researching a bug
Is it public?  I’d be curious to look at it.

> I was surprised that a newly created file was being replaced when
> being processed a second time
What created the file?  What king of “processing” happened after?

> I tracked the surprise to diff Lib/distutils/dep_util.py @ 57642:9211a5d7d0b4
> where a comparison with a resolution of 1 second was replaced by a
> floating point comparison
Indeed.  The whole distutils codebase should use ST_MTIME or st_mtime consistently.

> Using all floating point doesn't resolve the issue as OS timestamped
> files can have more resolution than python floating point may hold,
If I understand this bug correctly, it’s a platform-specific limitation.  We can try changing all distutils files to use st_mtime and see if tests break.  Would you like to work on a additional test case to reproduce your bug?