It could be argued that, during this particular time in Starfleet's history, they used an "NCC-??00" serial number in registries to designate an experimental or prototype model of the class, with incomplete systems or a test-bed platform, whereas anything with an "01" would be the first production
ship of the line, fully functional with all the bells and whistles.
This would be akin to using an "NX" in the registry later on. Granted, Enterprise's NX-01 and Columbia's NX-02 somewhat muddies that argument, but it could be counter-argued that that's what they did for a while in the 22nd century, and went to an NCC-??00 style in the early 23rd century for a limited period of time. Maybe some bureaucratically-inclined Real Admiral wanted some kind of token legacy and changed Starfleet policy to NCC-XX00 during the Connie's time. After he/she retired by the late 23rd, they went back to the more traditional NX designation, just in time for Excelsior's construction and they stuck with it ever since. Stupid bureaucratic nonsense like that happens all the time in the real world in the government & military. I don't think that humans evolved so much by the 23rd century not to engage in a tad-bit of occasional self-promotion from time to time.
This argument could fit nicely in the established continuity, as well as resolve the apparent conflict between MJ's statement and FJ's designs.