The piece you're missing is that the interpreter state holds a direct reference to the import machinery in interp->importlib, and *that's* what gets used by the builtin __import__ implementation.
I'm beginning to think the thing to do is to simply say "yes, there are two copies of importlib._bootstrap". By default, the compiled in one is used, but you can replace it with the on-disk one by appropriately editing sys.meta_path and sys.path_hooks.
Trying to hide it isn't going to eliminate the potential problems - it's just going to move the problems around (and likely make them even more confusing in the process).