Honestly i don't see how a naked GPU would be cooler than one with a good heatsink and thermal compound.
silly boy
he is refering to a naked DIE like the 7800/7900/8800GT use vs. the 8800 GTS/GTX which uses an IHS to cover the die like your cpu does.

an IHS leaves too much room for heat gaps between the die and the IHS.
thus that is why you see people taking the IHS off their cpu's. in general your only going to get 5 deg better temps but there are extreme cases where i have seen twice that in a temp drop.