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I did my best to classify those on pypi that were using `.pth` files. My initial search had quite a few false positives (and now that I look at it, completely missed `.zip`-based source distributions so there's likely some false negatives as well)
Here's the summary of the categorizations:
$ cut -d, -f2 < data.csv | sort | uniq -c
 2 backport
 4 coverage
 4 debugging
 2 demo
 9 encoding
 7 except-hook
 58 false-positive
 6 import-hook
 20 module-layout
 20 monkeypatch
I realized about halfway through that "monkeypatch" was probably too broad of a category but continued with that through all of them, the monkeypatch category contains a few classes of things: fixing third party libraries, disabling ssl (yikes!), adding some "features" to builtins / stdlib modules -- which unfortunately I didn't really classify properly.
There was a single .pth file that I deemed "malicious" since it completely breaks the `subprocess` module (`subprocess-run`) but other than that they all seemed ~mostly not the worst.
A lot of the `module-layout` ones could be solved with things provided directly by `setuptools`, or just be rearranging their distribution's files.
The raw data is available in csv: https://github.com/asottile/pth-file-investigation/blob/master/data.csv