I don't own one, but was appalled at the "value for your money" proposition when I auditioned a number of Fender Custom Shop models in the $2500-5000 range when looking to treat myself to a new axe with some of my annual bonus a few years ago; this is actually what got me into building Warmoths.
Quality wise, there's no real differential between the Custom Shop models and the $1200-1600 range of American Strats, and I'll be damned if I can detect any additional "quality' in even the most expensive "Masterbuilt" models. As noted above you are pretty much locked into buying versions of older Fender models, and paying a LOT extra if you want them to beat up the guitar for you before you buy it ("Relics").
I DO like the Fender Custom Shop pickups used in most of their models and use them in some of my builds. They are great reproductions of their vintage pickups and conversely are a good deal for the money if you're trying to get "vintage" Fender sound.
Many of the Custom Shop models DO have "real" nitro finishes; some have "Nitrocellulose lacquer over urethane finish", although I don't quite understand the point of that, unless they are using a top nitro finish without UV protectorant that will "yellow" over time.
If you're just talking wood; on average, all things being equal anything you buy from Warmoth will be of equal, and usually better quality wood than what you get from any Fender to include the Custom Shop models and of course you have a vast array of more choices than you do from Fender; if you're going to spend that much on an axe, it should be PRETTY!
Leaving "relics" out of the mix, you can do your own version of anything the Custom Shop puts out using Warmoth parts and have the same or better quality for a lot less money. For example, a '56 Strat Closet Classic is $2820 from Musiciansfriend.com, about the cheapest place to buy one. All the parts, to include the same pickups, would cost you $1182, but that includes a AAA Flame Maple top on the body in vintage 2-tone sunburst and a AAA flame maple Total Vintage neck with vintage gloss finish, and in this case I'll guarantee you'll have higher quality wood