Whether the Franz Joseph scheme, with the 500-range scouts and destroyers, makes any sense in either context is debatable. It's not supported on screen much, as the FJ graphics we see in the movies don't flaunt registry numbers.
The only thing I can recall "on screen" that supports Franz Joseph's NCC numbers is some of the communications chatter from the Epsilon Nine station in the opening scene of ST:TMP - They specifically mention the "scouts" Columbia
(I think it was Revere
, I'm at work and can't easily check atm), plus the dreadnought Entente
- all of which are referred to by NCC numbers which match the Technical Manual.
That's true, but even though some parts of the tech manual may be canon, that doesn't mean that all are, need be, or must be. Indeed, I can point to the misspelling Defiance
(and/or the absence of the Defiant
) as an error, to say that it's wrong on at least one point. If wrong on one, why not many? Additionally, the backstory of the tech manual given in the forewords creates enough room for any part of the tech manual to be fictional in-universe,
in any aspect that might clash with canon.