Of note: github can actually override this logic internally, in a way which they have not made accessible through the API: if you use github's merge button to squash or rebase-merge a PR, it'll be marked as merged, despite the PR's commits not being part of the target branch.
The issue seems to be that there is no provenance tracking. If a commit appears first in the contributed repo, and then makes its way into the base branch, I think that can reasonably be considered merged; if the contributed branch gets overwritten with commits already in the base branch, that is no longer a contribution at all and just the contributor resetting the branch (perhaps with malicious intent, or else through sheer ignorance).
0: https://docs.github.com/en/actions/using-workflows/events-th...
This is useful in many cases, but is still very confusing UX in such cases. Nothing was exploited, the PR update messages are just... well, poorly designed.