The dealer, and FCA, can make a case that by modifying your vehicle you caused a problem. However, their attempts to blanket void your entire warranty is not legal. Rather, if your modification causes a failure of an OEM part, then it's on you. If your modification did not cause the failure of an OEM part, then it's on them.
Let's look at some examples:
1. You install an aftermarket exhaust system and in doing so, one of the pipes comes in contact with an electrical harness. As a result, that harness burns and a serious short circuit results. This fries some modules and your LED tail lights. Is it on you? You bet it is.
2. You install an aftermarket exhaust system. Somewhere down the road your head unit fails to power on. Dealer claims your exhaust system voided your truck's warranty in it's entirety. Well, no...these two systems are not connected and that is total BS. The fix is on them.
Dealer's won't touch turning off MDS nor will they touch making any changes to the TPMS systems for that matter.