I was able to have my side sills repainted under warranty. If your car is under factory warranty, from what I understand it can't be the extended warranty. Your zone rep has to inspect it and then they will repaint.
Only problem is that your side sills will turn yellow again if they are not properly insulated.
This is what was done on my 1998 Viper:
Side Sills were repainted, but also stripped to the bare metal first. Cost was about $800.00 that was covered. My side sills were sent out to a place that does high end cars. The service manager didn't want their in house body shop to do it.
I also had the inside heat deflectors replaced with new ones and the rock tabs on the front of the sills.
As a precautionary measure, I took header wrap and cut it into strips and glued them to the inside of the sill by the cats. DO NOT wrap your cats. This seemed to work well and no color turn yet. I was told by the body shop that the VT paint would help a little, but not much.
My whole experience in this warranty work seemed to be subjective to your service manager and also the zone rep. I may be wrong on this, but it almost seemed like it was dependant on what mood they were in. If you need the zone rep to contact my rep, e-mail me. Bill Pemberton was a big help in getting my side sills done because of his knowledge of how to approach this.
good luck!