If you look closely at the warranty information, Ford honors the body paint for 12/12K for items such as chemical corrosion, or fallout. But the 3/36 warranty covers Mfg. defects.
My guess is that the dealer who denied the warranty fix is either misunderstanding the warranty, or just being #@$holes and using the fallout clause as their reason for denial.
Try another dealership.
Good luck,
David