But why stop there? Let's also remove the README.md from the repo. It can also have it's own independent revision history. Maybe they should also add a feature for managing the LICENSE file for you.
/sarcasm
Ideally both of those files should be under a `templates` section in the repository settings tab.
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.
I understand your overall point, but as a slight aside the wiki is a git repo: https://help.github.com/articles/adding-and-editing-wiki-pag...