Things like air filters and oil filters are covered by the Magnuson-Moss act. Though it won't stop a dealer from maybe trying to get out of something if given a chance.
I spoke with my service advisor before I changed out the muffler on my Rebel, he told me just as long as i didn't touch the cat, everything would be fine. Of course they won't cover the part we modified, but it wouldn't effect the rest of the vehicle.
As for the lift, my dealership lifts RAMs with both Mopar and aftermarket kits. They will warranty anything they do, even if it's a non-Mopar kit. Though this is more the dealership standing by the work and vendor they use.
To the OP, check if you dealer and other dealers in your area offer non-Mopar lift kits. Most I've seen do, or they use a 3rd party shop who specializes in lifts, usually taller lift than what Mopar has. They will always warranty those kits/lifts if they offer them.