If you break something abusing it off road then of course they will not cover it. Ford is not responsible for damage resulting from collisions, just like they are not responsible if you smash your diff on a rock in the desert; this is arguably abuse. Bolt-on mods are COMPLETELY different. I will say it again, cutting the exhaust will void the warranty on the exhaust but the rest of the truck's warranty will remain. Full stop.
Furthermore, the dealership does not warranty the truck, the warranty is covered by Ford Motor Company. For trivial things the dealer will go ahead and do the work but their warranty work is audited on a regular basis to make sure the dealership is not doing work that should not be covered (ie - breaking things off road or on a race track). Dealerships don't care if parts are warranteed or not, the only difference to them is who pays the bill, you or Ford. Some will go to bat for the owner and push to get things warrantied while others frown on mods but in the end the decision is not theirs to make.