A warning like this sounds good to me though I'd prefer it to be slightly more verbose, like:

"RuntimeWarning: '<module>' found in sys.modules after import of package '<package>', but prior to execution of '<module>' as '__main__'; this may result in unpredictable behaviour"

or it wouldn't really have helped me much to understand what was happening.

P.S.: You understood correctly that my own code is fixed (patch sent to the affected user, next release will have the fix). Learnt something about the whole __spec__ and double import subject along the way so it wasn't completely wasted time.