I'm not sure your auto-merge commits are really that ugly or if they really matter.
When I merge PR on GitHub I don't look at the individual commits. I look at the final diff. I often ask the developer to roll back some of his changes, and add some new. After he's done with fixes and pushes again, I look at the final diff again and the rolled back changes will be gone as if never happened, as far as I'm concerned.
Reading commit by commit is not practical when merging a PR. It's really best to look at the total changes. If I want to look at the details of a specific commit, I can guess that the commits with "auto-merge" in the comment are not doing anything interesting, I wouldn't look at those.
But if you really want to avoid these commits in the future, then do not auto-merge, but use rebasing instead. In the end, this is only a cosmetic issue, not a real problem.