Thanks for diagnosing this further Matthias. I think you're on the right track. For example, if I add this to zope.testing's d/rules, the bogus empty /usr/lib/python3.5/dist-packages directory does not get installed:
override_dh_auto_test:
dh_auto_test
rm -rf .pybuild/pythonX.Y_*/build/zope.testing.egg-info
So it does seem to be an artifact of running the test suite.
