You can see an example of the film on my car in a photo in
this thread.
This page says that the film has a UV inhibitor that protects the plastic itself (doesn't yellow or turn brittle) but does not prevent the UV from passing through into the paint. I suppose as long as both the film and the regular painted areas are equally waxed or polished then they should fade the same.
When I went for the clear film I thought about the fading issue -- my final conclusion was that if the paint on the car faded I was going to be unhappy anyway, regardless of whether it "matched" the protected area. Other parts of the car that typically do not get direct sun were going to fade less too, creating a look like grandad's Chevy II - with bleached out fender, hood and trunk tops and less faded sides. I just focus on keeping the whole car cared for well and have to trust in the UV protection of the polish (and the garage

) while enjoying the rock chip protection.
(edit - I guess eslai and I were posting just about the same time... good minds think alike!)