Yeah the game runs with that - the only thing I noticed was before I put Gambit in, MK's name came up to select him (not an image or mannequin just a black spot with a name of his), and today nothing to select MK came up.
Also - the saved file I had at the time had Ms. Marvel on my 4 player team and I noticed that she loaded with Gambit, but when I changed her out to someone else, she wasn't on the character screen to select after that - so she and MK must be in another slot that isn't seen - the invisible selection you're talking about.
But yes the game runs fine - no other isses with it or the characters off of that herostat file.