I'm guessing they're going to tell you they'd be more than happy to fix it, but that you'll have to leave the car w/ them while they send it to a body shop to completely strip it down and repaint it. I don't know if it's worth it.
I have a lot of "small" defects in my paint, like small nibs that probably got into the clear coat, but I'm not going to bother with them because of the overall inconvenience. How much does it bother you? Also, are you going to wrap the car? If you apply a PPF, there may be a chance that it hides some of it due to a minimal orange peel effect.
I don't know though, as I'm no expert in PPF. I do know several people detailers and PPF experts have told me that the PPF will hide minor swirl marks and the like. Only issue w/ nibs is that it causes bubbling in small spots. If yours is flat, I wonder how that would turn out.