I laugh every time I see a thread that the members say just return it to stock and take it to the dealer..NOT TRUE.
I own a company who does performance tuning on GM and Ford vehicles. [performance autosport] The first thing we tell our customers is tuning will VOID your Warranty. Even if the Vehicle is returned to stock the dealer tech can tell it has been flashed and will flag the car,If the dealer has any doughs there are several tests that can be done to see if the ECU has been altered.
People will also quote the Magnuson warranty act about the manufacture proving the damage but who has the time or money to fight them,plus it is clearly specified that a tune will void the warranty in the owners booklet.
IMO a tune is great for performance and if the warranty is not an issue than do it,but do not think you can get anything by the dealers these days ,the first time your truck is plugged in to the Ford laptop the first screen the tech sees is that the truck has been modded and when that laptop is updated by Ford all that info goes directly to there data base and your done.
Any major or minor repairs must be approved by the Ford warranty people and a rep will be sent out to look over the vehicle for any major repairs,the dealer is NOT the decision maker and if they fix it with out telling Ford first ,then the claim is denied.
All of my personal and shop vehicles are 100% stock with no ECU mods for that reason,if I wanted a fast vehicle I would not have bought a Raptor,I love my tuck but love the Warranty more.