You’ll want to talk to the PyPy devs. They’re been dealing with this for a long time so might have suggestions. And any proposal to restructure CPython to make alternative implementations easier will be much more compelling if it multiple alternative implementations all agree that it would work for them.
I believe that right now they use a merge-based workflow: they have a special branch containing pristine snapshots of the CPython stdlib, and from time to time they import a new snapshot and then merge it forward into their main development branch. This means they can carry local changes to the stdlib.
It would also be interesting to look at those local changes and see how well they would work in your prepared scheme, e.g. are all the patches in the “core” layer?