Quote from primetime:
Oh, wait a sec, now that I think about it, skipping the trace battle might break that file if the barrier doesn't go down. I'll have to check that out to make sure.
Yeah, I was about to say that, my guess is that it will either break the game or you will have to re-trigger it.
As for the desecretizing the room, I think that might work, I believe the Magmaul door is part of the main area. It still needs to be tested though, and it sounds like it might be hard to do. I think I have a saved game there so I might try it.