Sounds like everything here is not controversial, which is great.
Wouldn’t all setuptools single- or multi-file setup.py develop support be broken in exactly the same way, and in exactly the same way as PYTHONPATH or .pth techniques? It adds the source root to the import path, exposing everything in that directory. Unless you use a src/ folder in which case the path method is faithful to the installation.
Clearly Python import hooks are powerful enough to do whatever we want.
I like the idea of not requiring the editable wheel metadata to be the same as the production wheel. You could depend on a helper module or flag the wheel as editable. It would be a nuisance if multiple editable installs required different versions of the helper module though.