You yourself listed other solutions, including a per-game ability to disable notifications.
That's a player initiated action. The player shouldn't have to do this.
Am I - as a player - supposed to research for which games I should better turn off trophies? Why should I have to do this? Turning them off is just a workaround. Not a solution. The actual solution of mine is not buying PS3 games anymore. And also not buying a PS4.
Let's say GAF had some audio code, that screamed every 10 posts into your ears that you just earned a trophy. But you can't disable that for GAF alone. You would have to turn audio off for everything you do. So actually you would have to switch audio off and on depending on what you are doing. That wouldn't get on your nerves, wouldn't it?
The developer STILL have to create a silly checklist with stuff to do. The developer is not able to simply not have any trophies at all. Why is that? Why is anyone okay with this? Sony doesn't force rock solid framerates. Sony doesn't force 720p+1080p. Sony doesn't force quality control. But Sony forces that everyone adds trophies. Sony doesn't even force anyone to include trophies, that are actually achievable. This doesn't make sense.
I don't think that the original developers of Ico, Shadow Of The Colossus, Silent Hill 2 and so on would have been fine with this checklist stuff. It destroys the atmosphere in those games. And it's also not just about notifications. The player shouldn't get a stupid checklist with things to do for every single game.