Problems depend on the dealer. My dealer is mod friendly and I don't use the other one that isn't.
I went in and asked what would happen if I changed to a lift and bumpers and they said great have us put them on for you. I even asked 2 different service people and the manager, he now likes my Jeep a lot and wants it parked out front....
Does that mean he will cover the broken spring or wheel stud, no that is an option and not covered, but all of the rest of the Jeep is.
Ask them and see.