Good point. There is an exception in that act that allows the warrantor to waive coverage if the damage was caused by the consumer, so I guess Dodge can do it because the software mod in that case is causing the vehicle to perform outside of its design envelope. The warranty only covers manufacturer defects, and forcing the vehicle to do something it's not intended to do is not a defect.
So, I guess these Tesla hacks should be fine so long as they're only enabling things that the vehicle has been designed to do.
