Harley has been getting more and more pissy about authorizing paint warranty repairs, and that's after already being among the worst I've dealt with in the first place. They really do have some silly standard they use to deny coverage, based on how far away from the part you can still see the defect. As one who spent more than a few years on the manufacturer side of this issue in the auto business, I fully understand that cosmetic flaws in areas that are not normally visible shouldn't carry the same weight as flaws on what we called the "A" surfaces, which are easily seen by anyone. But I've seen Harley try to use that same BS on surfaces that aren't hidden but rather right out in the open. Such as an obvious off-color spot under the clearcoat on the upper side of the fuel tank. As the quality has gotten worse, and therefore the warranty costs have gone up, Harley has been looking for more and more ways to avoid paying warranty claims, and not just on paint.
With a flaw on the bottom of something like a saddlebag, I can't say I would approve replacement of the bag if I was the rep either. But I would authorize a spot repair or at least try to find a way to satisfy the buyer of a brand new bike. If Harley doesn't step up, I would suggest you offer that option to the dealer.
JMHO - Jerry