As a facebook user, I'm happy I'm not longer gonna get "your friend has invited you to this app..." notifications. As a developer, though, I can see why this would be frustrating.
Also, it's not like they have carefully selected the group of friends that they want! The ones I have seen just have a "Send to all friends" tickbox.
Create something people actually want and you won't have to spend your life trying to exploit every possible loophole in Facebook's system.
The problem is that creating something that people actually want, working via the channels that Facebook provides for people to access the Social Graph is very risky, as they can move the goalposts at any point.
So many new apps launch that banning notifications by app gets tedious. They all suck in different groups of your friends, so banning notifications by friends is tedious. Not forever, perhaps, but long enough to make you think ill of Facebook.
We've been there before, and even though as a developer I miss it, it was the right thing of Facebook to do.