Again, what is the use case? That's a real question, I'm not saying it to dismiss your ideas or points of view. It would be very much easier to think about a concrete use case, rather than making a general system for the sake of how easy it is implementation-wise. (The implementation might be easier now, but it might change, and there's a cost to keeping the generality in mind when designing things on top of all this.)

Something like the slot you mention can always be added later if it's needed. Is it needed now?


Also, the PyModuleDef should never be modified (beyond the one-time initialization that sets ob_type -- that's a workaround for not being always able to declare the type statically).
It should be possible to make additional, independent module instances from a PyModuleDef.