I also find this frustrating. Every time I want to add an app to Github, it defaults to org wide. So far, I've managed to keep the reins on that, and nobody has made a mistake, but I am just waiting for the day someone adds something org-wide that shouldn't be.

Another rant(ish). You can request a PAT for, say, 30 days for a repo, and if you don't have access, it'll prompt an admin to approve that PAT. Okay, makes sense. But then you can refresh that same token without permission going forward.