Have you come across `git rebase --update-refs`? This automatically moves your "intermediate" branches during a rebase and sounds like it could be useful in your situation.
There's also `git rebase --onto`, which effectively does the reverse - you tell git you've already rebased the part of this branch that overlapped with the "intermediate" branch, and it just needs to take care of the rest.
Oh that sounds exactly what I need to simplify the workflow I described for the multi-PR use case. I'm going to try that out today, I just happen to have a use case for it ready to go :)