Might not be the foam...in fact, I'm inclined to think it isn't. Saris has probably sold hundreds of thousands of those things, and I've never heard of a staining problem. We had similar staining (actually mild pitting, just in the clearcoat) from a Rhode Gear rack years ago, and we finally determined it was from tree sap. I left the rack on most of the summer, and over the months the tree dripped on the trunk lid. It apparently collected around the pads and ate up the paint. If Saris isn't seeing this on lots of other cars, I'd say they've done as much as they should.
But they could be lying. Maybe it happens to everybody...