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.
This was my bugbear for a long time too, and then I found fzf-git.sh (actually its PowerShell equivalent, PSFzf).
fzf (absolutely incredible tool with many uses) gives you fuzzy searching of anything you care to name, and fzf-git combines this with shell key bindings to let you pop up a fuzzy-searchable list of branches/commits/tags/whatever while typing your fixup command, then paste the object you select into your in-progress command line.
No more counting commits in log output to know how many ^ to put after HEAD, or copying out segments of commit SHAs!