If you do the glitch to skip the game to complete New game Plus, you still get forced to play as cat woman at the very end for the actual very last mission where you go to the museum to retrieve your things from Two-Face, but if you do the game skip glitch at the beginning you are no longer able to open the doors to the museum because you never actually got to or played through the part were Batman unlocks the doors with his hacking device. If I were to play new game plus and play it up to the point of just unlocking the museum, then do the skip, would I be able too just fine and not have anything else to worry about (and also be able to complete all the side missions as well on that same new game plus save file, going for the Perfect Knight day 2 PS trophy)

The big skip also breaks side missions, which you need to do in NG+ get that trophy.

I strongly recommend not attempting any skips in a casual/platinum playthrough, it's way too easy to break things if you don't know what you're doing.

Got ya, after completely screwing up two game files that I had already completed the original story on, I was thinking I might just have to stop going for glitches 😭