I have the same situation and can't find any explanation in the above posts or answers. For me it seem to be something within the GitHub way of describing "git log" between two branches.

I've made sure in "gitk --all" that the difference between my "feature" branch and "base" branch are actually only my commits. (Also verified the remote hashes to be correct between my local references and GitHub)

So regardless if I update my "base" branch on GitHub the base for my PR seem to be unchanged and include also the merged changes from others.