I have had trouble with GH displaying the correct diff. I guess in most cases I don't really want to merge branch-2 into branch-1 either, I want to merge them

I have had trouble with GH displaying the correct diff. I guess in most cases I don't really want to merge branch-2 into branch-1 either, I want to merge them both into master -- but first branch-1, and only then branch-2. I don't know if that's the use-case the third party tool is focused on? When I try that with github alone, which I have... it just gets really messy. Sometimes I need to switch the PR to a different random base branch and then back to the actually desired one to get github to update the diff when the base branch has changed since PR opened.