Those aren’t “substantial use” those, just “incidental”. I’m under the impression that the only characters they have the rights to are those featured in attractions, M&Gs, and locations (like restaurant themes). I don’t think they have the rights to use Iron Man, Thur, etc just because they are depicted in murals
That "crash site" thing in the middle of the land across from the spiderman entrance is exactly why it's there. It represents all the characters Universal has rights to. It's not considered incidental.