Some of the weird things I see are perhaps the consequence of running Emacs
in place from the build tree.

It is assumed that normal users have write access to
native-lisp/VERSION-xxxxxxxx/, but not to
native-lisp/VERSION-xxxxxxx/preloaded?

The function already deletes any *.eln file in a stale native
VERSION-xxxxxxx directory, just not the ones in preload/