Per the Magnuson–Moss Warranty Act, adding aftermarket equipment (including what would be the factory dual alternator setup if so equipped) won't legally affect the vehicle warranty unless Ford can show that the added equipment caused the problem. Of course, the aftermarket bits themselves also aren't covered by the standard vehicle warranty.
The law doesn't stop unscrupulous dealers and companies from attempting to get out of warranty work, but the legal requirements are pretty clear. They aren't allowed to say "You installed a second alternator, therefore we're denying warranty coverage on your failed windshield wiper arm" or whatever.