I emailed Fender yesterday. Today they sent me this:
The American Vintage II instruments have a Nitro finish with a Polyurethane undercoat/sealer. It's important to understand that all Nitro finishes are prone to aging and wear over time, including checking as you mentioned. It's very possible that the finish could wear off over time with changes in humidity and temperature as this is a characteristic of Nitro. Many guitar players enjoy the fact that the finish looks more and more worn and vintage over time, others prefer to go with something much more durable such as a Gloss Urethane finish. The Polyurethane undercoat/sealer however does make the finish more stable than a 'thin-skin' or 'flash' nitro finish which is majority nitro and found on a few of our instruments, such as the Hot Rod series. Of all the nitro finishes, this one is definitely more vulnerable than the Nitro with Poly undercoat/sealer. This article may provide some more information for you regarding our finishes: What Type of Finish Is Used on Fender Guitars?.
The nitro over poly sealer has been used since the 60s, according to a link someone posted above.