Most of the warranty decision is not made by the dealer. The PCM monitors countless functions of the vehicle and will take a snapshot of any event that is out of factory specs.
Let me try to explain it this way. I had a customer with a Focus ST that had low compression on 2 cylinders and wouldn't run. He swore up and down it had never been tuned. Which it turned out he was correct. However he had put an aftermarket BOV on that was adjusted way out of spec. So the car was producing more boost at certain load percentages than it was supposed to. So every time this happened the PCM takes a snapshot. Date, mileage, engine temp, rpm, load percentage, etc.. So when Ford requested data files from the PCM on this car they denied the warranty claim. The customer had also cut the cats off and was running a short straight pipe off of the turbo.
So the PCM tracks everything. Even a pedal commander which doesn't reprogram the PCM will produce traceable snapshots every time the truck is producing more specified boost.
So any type of performance mods like a pedal commander or tune can affect a warranty repair. Ford extended warranty is the same as the Factory warranty. So that can affect your coverage on extended warranties also.
Years ago when we had the 03' Cobra's if we had a drive line failure it wasn't uncommon for Ford to send an FSE in to inspect the car for mods. They used to put us through training to detect if a car had mods done to it. Back the it was the dealers responsibility to tell Ford if the car was modded. Of course most dealers didn't. Dealers wanted the warranty work AND they didn't want to **** of their customers. So if Ford would pay and the customer was happy in the end it was a win win for everyone but Ford. However if the dealer got caught doing that Ford would not only kick the warranty claim and refuse to pay it. That would also end up with the dealer getting warranty audits more frequently.
We replaced a motor in a 2008' GT500 that one of my customers blew up. We couldn't detect any mods but when Ford got the blown motor back they felt it was modded and refused to pay the claim. So we were out something like $15k.
So as mentioned above. Be prepared to pay if you make those decision to mod the truck in certain ways.
Now with that said if you tune the truck and the AC compressor goes out both factory or extended warranties won't balk at paying that repair.
So a tune doesn't just void your warranty.
Also as said above if Ford denies the claim goo luck fighting them and saying THEY have to prove that your mod cause the failure.
Well put, this should be copypasta for anytime anyone asks about warranty.
Also @xxaarra 5star sells a warranty with their tunes if you are so inclined.