I understand this is chaos, but it's chaos because it has to be. There's no way to move users from an world of opaque "if it's an application, it can do anything it wants" to a world of "applications should ask me when they want to do something" transparency. The idea that Apple doesn't care about the Mac because it's trying to explicitly improve our privacy and security is … weird.
Apple could have figured out a way to coalesce all the individual pop-ups into a single window. I'm sure they considered it and deemed it not worth the effort since this is a one-time pain... of course it's one-time pain shared by millions of users. :-(
I doubt any regular user is going to see anywhere near this amount of warnings.