Tourpak on my 09 SERG came in bad, they had failed to sand the base and it was peeling. I used it while another was ordered. Dealer then returned it to HD warranty department. Never any discussion to repairing it. Fender on my SEEG was chipped by shop while doing totally unrelated warranty work, they got me a new fender and installed. But I used the chipped one for 5 weeks while new one was on order. Once again, never any discussion to repair.
If HD let the Dealer send parts out for repair/refinish work then they would be obligated to warranty a off-site vendor's work, which they have no contract with, you can bet HD is not going to let that happen. Someone is going to pay for all come-backs and it is not going to be HD and if Joe's B/S did the work what leverage does HD have to force them to cover a problem? So ask your dealer what the procedure is, they have no reason to not tell you.