One thing people fail to realize is that the manufacturer is relying heavily on the dealer to tell them about the vehicle. If the dealer tells them you put a 12” lift on your truck while signing the paperwork to buy it in the parking lot then that’s what happened as far as they’re concerned. Yes you can modify a vehicle and still get warranty work as long as you have a good dealer and have a good relationship with them... they can and will get things glossed over to help you. It shouldn’t be this way but that’s just how it is.