The PEP says the goal is to span packages across directories. If you
split something like zope into multiple directories, does having a
separate zope.pth file in each of those directories really cause a
problem here?

I think pje already answered this: yes, you do split zope into multiple packages. But then, you may install all of them into the same folder.
This has caused pain for Linux package management tools in particular,
because they dislike if to packages install the same file. So if you
can arrange the pth files to have non-overlapping names, you can still install them into the same directory, and dpkg is happy.

Regards,
Martin
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