Reclone from master (or the active branch if something else) to another directory, merge in their final changes, manually if needed, properly test the result, and sent a new PR with the cleaned up version?

(caveat: I've not used git in anger, there may be more to it than that, but I can't imagine much more)

I suppose who is responsible for dealing with cleaning up updates before merging them into the main project depends upon who wants it merged most: the PR submitter because they want a fix/change/other in upstream so they don't have to maintain their own fork, or the project maintainer because the update is more generally useful to other users or more specifically useful to the maintainer.

If you submit a badly arranged PR or other patch you are creating extra work for the project maintainer(s). Depending on the project and maintainer(s) this may be acceptable or, equally rightly, it may not.