> I want to edit a service to harden it for example. Oh, wait I shouldn't edit it directly with vi? Because it gets overwritten by package updates.

I don't think you're supposed to edit anything inside /usr, except perhaps /usr/local, but even that has a better alternative in the form of $HOME/.local, which is a well defined standard at this point.

Maybe I'm unaware or mistaken but if you're editing anything inside /usr as a normal user, you're either using Linux wrong or doing something unexpected or unusual. This is why requests to make GUI file explorers have root escalation capabilities sound absurd to me. I can't think of a reason why one would need root access when using a file manager, especially a GUI file manager.