A small number of the "connies" (in Court Martial) did have hull numbers that were in sequence, but those might have been an exception.
Greg Jein assigned those registry numbers in Court Martial to the known TOS Connies, but there's no canon evidence whatsoever that that's what they were supposed to be. I myself have a hard time believing that almost every Connie Starfleet owned just happened to be at the starbase's repair shop at exactly the same time.
Tribble Herder wrote:
Anyway, there are plenty of structural differences between the eleven footer and the AMT model, so it's pretty easy to justify the Constellation being a different starship class, say the one immediately preceding the Constitution class. The lower registry number plays directly into that.
The Enterprise-B has structural differences from the Excelsior (and far more than the differences between the TOS Enterprise filming model and the AMT kit), and yet they're the same class.
Also, it hasn't been canonically established what the U.S.S. Constitution's registry number was. For all we know, it could be NCC-1000, and as such, there wouldn't be a problem with the Constellation's registry. And that's even if you abide by the theory that registries are chronological (Yes, I'm well aware that there's a list somewhere that states NCC-1700 for the class ship, but it's never been shown or referred to in the show).