A couple more bugs.
The scene where your party members rejoin you before the last boss can play multiple times. Last boss and true last boss can still be accessed fine as far as I can tell, and I didn't see any glitches on my party.
Metal Tower V1 can be skipped. Leaving immediately starts the Earth Tower V1 storyline and prevents you from going back to Metal Tower V1.
You can do weird things with Eirin's Shady Drug during some the scripted fights. I didn't manage to find anything gamebreaking during any of them though.