Well I am pretty sure the PS3 game was not emulated at 100%, some code must have being rewritten for PS3 : native 720p + locked 60fps on PS3. Also it's still one of the most impressive title on PS2, and used all the tricks the PS2 had, like using the PS1 CPU to do graphic tasks.I'm pretty sure it was emulated, since the PS3 version was done with emulation. I think the reason they did it was it was less work than writing PS3 support for naughty dog's custom language, which was basically designed around the ps2, if I understand right. Plus, Sony probably let them use their official PS2 emulator to start with.
The fact that a ps2 emulator can run on a downclocked Cortex-A9(what was the clockspeed again ~300MHz?) even at half speed is pretty incredible. PCSX2 wouldn't get anywhere near that, especially running the jak games.
I mean, the fact that they sold it like that is pretty lame though.
If that game could be emulated that perfectly, while increasing the resolution (and not an easy 4x increase like PS2 games on PS4, but an odd 640x448 to 1280x720), all PS2 games could have being easily emulated on PS3.