Yes, but it's not even just an end-user problem. Github is taken as assumed all over the place, for example Golang projects often directly download their dependencies from Github.

That is their problem. They should not rely on Github, especially now, that it is owned by MS.

Right, but instead of defeatism, people ought to start self-hosting sooner rather than later.

Is there a framework for putting the issues and PR's in the repo?

You can self host open source alternatives such as Gitlab