So... with the current analysis, let me tell you something I'm 100% sure about:
Star Fox 2 Final is much harder than the leaked ROM.
No more lock-on (!), AI has improved, Corneria damage seems to be higher (possibly more random), Miyu and Fay don't have a double blaster anymore, and collisions are working actually better.
Basically, there are gameplay differences (more significant than you would think), definitely more polish, and the finetuning that Dylan Cuthbert was talking about is indeed there.
...just the fact there's no more lock on and improved AI means that I will take much more time to actually beat the game. As far as I'm concerned, I expect the gaming experience to be widely different from what I've played in the long run.
This has convinced me that they're not joking around, I expect Star Fox 2 to be as hard as Star Fox 1.