I don't see how there is any other way to achieve this cleanly, it's not a git thing, it's a logic thing right?
The update branch button works normally when I don't stack the PRs, so I don't know. It just feels like a half baked feature that GitHub automatically changes the PR target branch in this scenario but doesn't automatically do whatever it takes for a 'git merge origin/main' to work.
Those are not hallucinated. PR B still contains all the old commits of A which means merging would apply them twice. The changes in PR B are computed according to the oldest commits belonging to PR B and main which is the parent of squashed A. That would essentially means applying A twice which is not good.
As for updating PR B, PR B doesn't know where PR A (that are also in PR B) ends because PR A is not in main. Squashed A is a new commit and its diff corresponds to the diff of a range of commits in PR B (the old commits of PR A), not the whole B. There's a lot of metadata you'd need to store to be able to update PR B.
I don't think we need to store any additional metadata to make the rebase just slightly more smarter and able to skip over the "obvious" commits in this way, but I'm also just a code monkey, so I'm sure there are Reasons.
Git store all its information as a directed acyclic graph (a tree) of commits. The leaves of that tree have names, and are what we called branches. Each commit points to a tree (also a tree data structure) where the nodes are blobs (files) and sub trees. But that tree only stores the files that has been changed since the last commit. Git does not store diffs. Diffs are computed as needed.
This why the common ancestor commit is important. From there, a version of the working directory is computed for each branch (main-with-squashed-A and PR B). Files that have not been changed since PR A are ok, but everything else will be different, especially if you’ve modified the same lines.
Squashed A is a brand new commit with a new tree that PR B does not know about. You need to recompute PR B on top of Squashed A, (which will create new commits for PR B).