Here is an updated patch. Since the message no longer applies to top-level modules, I went back to a version closer to Wolfgang’s suggestion, which should eliminate the problem with “any parent packages”.

Now the messages look like this:

/media/disk/home/proj/python/cpython/Lib/runpy.py:125: RuntimeWarning: 'package.module' found in sys.modules after import of package 'package', but prior to execution of 'package.module'; this may result in unpredictable behaviour
  warn(RuntimeWarning(msg))
/media/disk/home/proj/python/cpython/python: Error while finding module specification for 'package.module' (ValueError: package.module.__spec__ is not set)
[Exit 1]