Same here - GTA 4 updated without any problems.
I'm still on 3.10 and didn't get any PSN prompt - just a prompt about there being a patch available.
I'm sure sony don't allow it (you know the whole "your game & patches must be checked by Sony to ensure you meet our standards" thing - i.e. we need to check to make sure you have not introduced an exploit!), but i did wonder if 3rd party games pathes are hosted by the 3rd party devs? (i.e. only Sony developed games have patches hosted by sony?)
Either way, doesn't really bother me - i'm sticking with 3.10 for now.
Yea I think it gets updates from the publisher's servers. Dragon Age for example also logs into the EA servers to get updates from there, but of course when u buy/install any DLC, you can only get those thru psn. Not sure about Sony specific releases, as I don't have any to try out. Maybe someone else on older firmware can confirm?