I think my MANIFEST file is working. The only files that end up in the archive are the files specified in MANIFEST, plus
their metadata. Interestingly, these metadata files do not really exist before making the archive, they are somehow created in the process:
$ ls -la | grep Makefile.PL
-rw-r--r-- 1 planz planz 577 Jun 15 18:53 Makefile.PL
$ tar cf test.tar Makefile.PL
$ tar tf test.tar
So, I think if I want to stop having these metadata files in the archive, I need to pass some Mac-specific flag to the tar program. But tar --help did not reveal anything useful (just the regular GNU tar description).
My current work-around is to make the bundle on a Linux machine. Using a pre-Tiger OS X should also work, as the metadata-preservation seems to be a new feature.