Imho GitHubs pull requests shouldn't be used as a replacement for good commit messages or code comments - GitHub might go away, you might decide you don't like them anymore or whatnot. If you feel like someone raised a question about some part of your code in a PR that does have an answer that's only obvious to you, there's no harm in just adding another commit adding comments to the code (you can even squash that commit into the commit changing the code between merging to master and pushing).
