I've never worked in bike shop so I don't know how bikes come in, but I've looked at lots of new bikes and have never seen any chips or marks on the paint, so if I did buy a new one and it had a chip, I'd at least like money off or get a replacement. It would just annoy the hell out of me to see a chip on my NEW bike every time I went to ride, even though it probably would eventually get scuffed up. I remember I got a nice new Trek mtn bike over ten years ago, i was so anal for the first year about keeping the frame looking nice even waxing it, having a big scratch or chipped paint would have ruined the entire new bike experience. Same thing goes with new cars, or just about anything new.
I won't be surprised if the guys that work there give you a hard time, to them its just another bike that works and looks fine, but just be really nice and show a lot of appreciation...