The day I got my phone (launch day) I kept the factory protector on the screen until I bought a screen protector. As the protector was about to be put on, the installer (Best Buy) pointed out a micro scratch on the screen. Sure enough, there it was. I asked him to hold off installing the protector while I decided how to handle things with Apple.
I made an appointment with the Genius Bar, took the phone in, and under what I suspect is “special” lighting in the store, the scratch was invisible. I spent my wait time (15 minutes?) looking for it and couldn’t spot it any more. When the Genius came out he took out a keychain flashlight and was able to find the scratch, but it appeared much more minor than I remembered it. He offered to exchange the phone as it was within the 14 day window. I felt a little silly exchanging it over such a tiny flaw that would be made basically invisible once a protector was installed...and since I’ll trade the phone in in a year, why fuss?
I left with my original phone and went back to Best Buy for the installation of the screen protector. One again, under “normal human lighting” the scratch was very visible. At that point I just said screw it and had them put the protector on.
So I have to say there does seem to be something to this scratching business. And I learned something about the lighting in Apple Stores...