Truly odd that there was fading with the guitar in the case.
I have two blue/purple PRS'. They're cased when not in use. One is a PS Limited run in Northern Lights, the other is a Special with Artist Pkg. in Aquableux Purple Burst. The Northern Lights PS guitar is 6 years old. I can't see any discernible fading. The Special is about 8 months old. Again, no fading.
Knowing how photosensitive organic blue and purple stains are, I'm pleasantly surprised. I expect that some day there'll be some fading, but maybe I'll be dead by then.
PRS does indeed warn customers about fading in its warranty that expressly excludes fading paint from its guarantee.
On a personal note, blue would have been my last choice in either one of these guitars, but I like the way they sound and play, so I figured WTF, if they fade, so be it.
Photosensitivity isn't about exposure to air, it's exposure to light. So it doesn't matter how thick the clear coat is. If light gets through, it will affect the photosensitive chemicals underneath the clear coat, similar to the way photographic negatives on glass plates were developed in the 19th C.
It should also be mentioned that all organic dyes are somewhat photosensitive, even the ambers, browns and reds (a lot of early Les Pauls had the red burst fade to brown, for example). These dyes fade a little more slowly, but one thing that makes the fading less strange-looking with these colors is that even faded ambers, browns and reds still look pretty good with the natural color of wood, where blue colors look a little strange (to me, anyway).