+1.If your dealer says they will cover a modification, get it in writing. Ford has the final word on coverage and can override what the dealer tells you.
Ultimately, when an item fails, your dealer does the repair and submits a warranty claim to Ford. Ford then re-imburses the dealer for the part(s) and labor. For the most part, dealers want to keep their customers happy and fix whatever breaks on their cars. I don't think the dealer looks for ways to get out of repairing it. After all, they are getting paid (just by Ford, instead of you). And yes, the warranty labor rate is a little less; but, at the end of the day they make money and it keeps the service department busy. The problem arises when something breaks and there's the chance Ford is not going to re-imburse the dealer. Let's be honest here, if you grenade your '13 662 hsp engine due to an aftermarket tune that was a tad too lean, whose fault is that? It's yours and why should/would Ford pay to repair it. Also, your dealer can be as mod friendly as they come; but, I guarantee the minute they try to get authorization to replace a blown engine in a GT500, Ford will deny it until a Ford Rep inspects the vehicle, engine, any aftermarket parts, etc. to ensure they're not paying for someone elses mistake. Just be prepared to pay if you want to play.