The problem isn't that it's just one file (actually 2 if you're counting pr templates), the problem is we're just going to continually get this pollution of the project because it'll become "acceptable." Slippery slope and what not.
I mean at this point why is the wiki in it's own space and not git versioned? (Put it in github-wiki folder!) Why have separate gh-pages as well? (Just stick them in github-web folder!). Just shovel everything into one git repo. Don't forget the .githubconfig file in case you want to programmatically config a repository instead of going into it's options menu. And on, and on, and on.