I think there are decent workarounds but it is still quite time consuming and error prone for me to keep up with everything.
I wasn't aware notifications were "broke" or working any differently, I guess that would be a big deal though.
I was thinking the same thing with the followers/following tracking unread posts/time visited, problem is as far as I'm aware none of that type of data is tracked.
When I first started here - just in June this year - you would get notifications for comments people had made. Chrome also had popup notifications for when people commented. No idea how it works I admit but I'd like to see it fixed then leveraged so you can get notifications for when people you follow post things. Then I wouldn't miss as much :)