Even in that case, if you're manually editing anything inside /usr either by being root or by using sudo, you're doing something wrong or unexpected.

Anything inside /usr should only ever be modified by the package manager, not by the root user, or any other user for that matter.

If you want to make system wide changes, make them in /etc. If you want to make user specific changes, make them in $HOME/.config, $HOME/.local. Your package manager should never overwrite anything in /etc or $HOME. If it does, it's a bug.