AFAICT using hard links only serves to save up a little time and disk space; it seems to me that always copying would solve one or two bugs at a small cost (not so small for large projects, I don’t know).  Could this impact setup scripts?  Maybe if os.link were monkey-patched and expected to be called.  I could ask on distutils-sig.

In #15205 Ollie noted this: “distutils2 appears to always copy instead of hardlinking resolving all of these issues”.  That would be because d2 uses shutil.copytree and distutils.util.copy_file (yes, a function from distutils1 because of some Windows issue :().