The Mod Shop experience isn't offered here in the Netherlands, and the way Fender designed their site the configurator can't even be accessed from here, as much as I'd love to have some fun with it
I do own a Mod Shop Jaguar (g**t*r, sorry) but I bought it used so I can't comment on the experience of ordering one.
Mine came with a spec sheet that doesn't fully match the actual build. For one, the sheet mentions a bound fingerboard but it doesn't have one - and it probably never was an actual option for lefties. It should also have V-mod pickups but the ones actually in it appear to be some kind of 1962 reissue pickup with bevelled polepieces and cloth wire. I'm pretty sure the neck is the actual one it came with, because there is no other way of acquiring a 24" scale lefty 60s spec C-shape Fender USA neck with a 9.5" radius outside the actual Custom Shop or the Mod Shop. It's a fantastic guitar by all means, with impeccable build, fit and finish.