I've done more work breaking down the findings:

pygoogle (7): All forks of a project of the same name. Ignorable since the name matches the project name.

cancelbot (3): All forks of a project of the same name. Ignorable since the name matches the project name.

Numeric (8): All projects seem to be peripherally related to numpy, but probably had their setup.py copied from an earlier version of numpy.

Aeosa (58): The most recent activity is all in one repository, so I've filed [mattneub/appscript#14](https://github.com/mattneub/appscript/issues/14) to request the change.

quasi (7): All forks of a project of the same name. Ignorable since the name matches the project name.

Motion and Graph (2): Two projects in https://github.com/scanlime/navi-misc. Ignorable since the name matches the project name.

Ohai (1): Made a comment here (https://github.com/bukzor/ohai).

NumPtr (5): The project makes the comment "I want to be able to remove them if I screw up this script; 'Sandboxing', if you will" and uses extra_path with the same name as the project; ignorable.

eispice (3): All forks of a project of the same name. Ignorable since the name matches the project name.

rtaudio (1): All forks of a project of the same name. Ignorable since the name matches the project name.

pyryutil (1): All forks of a project of the same name. Ignorable since the name matches the project name.

pbs (~5): Several projects are using the 'pbs' extra_path to group their packages (https://github.com/search?utf8=%E2%9C%93&q=extra_path+pbs+filename%3Asetup.py&type=Code&ref=searchresults), even going as far as creating a setup.py.in template with that setting. I've posted a ticket with what I believe to be the parent project.

korean (1): Uses the feature for load-time import. I've posted a ticket suggesting the removal of that.

kodos (6): All forks of a project of the same name. Ignorable since the name matches the project name.

pygraphics (4): All forks of a project of the same name. Ignorable since the name matches the project name.

pythonutils(1): All forks of a project of the same name. Ignorable since the name matches the project name.

Spike (2): All forks of a project of the same name. Ignorable since the name matches the project name.

timml (2): All forks of a project of the same name. Ignorable since the name matches the project name.

orange-bioinformatics (1): Uses extra_path to set a custom destination dir for the package. I've filed a ticket referencing this one.

pyNameList (1): All forks of a project of the same name. Ignorable since the name matches the project name.

FontTools (42): All forks of a project of the same name. Ignorable since the name matches the project name.

flopy (1): All forks of a project of the same name. Ignorable since the name matches the project name.

At this point, I've gone through 11 of the 54 pages of (most relevant) search results from Github. I suspect that's a good enough sample to determine if this feature does indeed need to be retained.