Earlier quoted context omitted.
Uhm, yes I would rather not have it in my repo. As to whether or not I want it tracked/versioned, that is completely outside the workflow for versioning in code in a repo. You can maintain a "version" of this separately ala Wikipedia's edit history, or even just have a hidden separate git repo for these things if you must use git. They already have this with gists. With lint configs or npm configs you can argue that…
I totally get where you're coming from. An extra file in your repository is quite the burden. This template file is the straw that broke the camels back. It should be removed. 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
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.