That is not right and it just lets them breed more incompetence. And while you are all telling me, 'oh, just take the repair.' The funny thing is, my factory paint warranty will be null and void after this job takes place. But, it's okay because the body shop will warranty their work. Nice!! And how is that fair? Anyone?
Actually, the repair would only affect warranty claims in the affected area. If you have a paint problem on say your hood or roof, it would still be covered by the factory warranty. That's only fair - since Ford didn't paint the door, they can't be expected to warrant it. The factory warranty on paint is only 12 months or 12,000 miles anyway so it's usually not a concern.
The bigger problem may be that the paint "treatment" that you purchased has already voided your factory paint warranty. The Ford warranty specifically disclaims warranty because of customer applied chemicals (you didn't apply it but it was applied on your order and not by Ford).