I'd have assumed that most people putting chips on their engines were pulling them off before having the dealer do any warranty work (I could easily be wrong, though). I haven't read Ford's dealer agreement, but I assume it holds the dealer responsible to enforce Ford's warranty policies. This service manager actually sounds like he's doing you a favour by recommending you take the vehicle to another dealer during the warranty period. He can't legally and ethically charge Ford for any future drivetrain repairs, because he knows about the chip. Another dealer won't have that problem. Sounds like good customer service to me.