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Doing a quick search on Github, it seems there are [537 projects](https://github.com/search?utf8=%E2%9C%93&q=extra_path+filename%3Asetup.py&type=Code&ref=searchresults) indicating `extra_path` in their setup.py. Many (most?) of those are using the feature to group packages into a namespace (Numeric, pygoogle, aeosa) in the filesystem. For each of these groups, it's probably worth contacting someone in the group to reference this ticket and get feedback.
Some of those projects just reference the value but set it to the default (disabled) or it's commented out.
At least one is using the feature for a load-time behavior injection (https://github.com/jwasinger/mailman_cas/blob/2ad0631001cb57366bb2a3b9d5f8eeddf5472c4e/mailman-2.1.12/misc/KoreanCodecs-2.0.5/setup.py). In that case, I don't think distutils should remain complicit in the hack, but the hack should be owned entirely by the project.