ENT says Humanity accomplish little (warp drive wise) for several decades following Cochrane first flight, while the preceding Trek series suggest there was more and it was fairly quick.
ENT says warp engines remained slow. But the other shows speak of great range, which is a different thing. The warp two-minus Boomers could well have covered the reputed distances in the time allotted, save for the ones deemed "impossible" (to the edge of the galaxy, least of all in just the few years between "over 200 years ago" and "200 years ago").
The Bonaventure isn't credited with either aspect: we don't know how fast she was or where she went. Heck, the Delta Triangle is so (in)famous that it might just as well sit right next to Earth, perhaps being a remnant of that other next-door mystery region, the Delphic Expanse (T'Pol's demolition team may have missed exactly three Spheres...).
So Human starship in federation service accommodated their new allies by switching around their registration numbers.
The Okudagrams suggest the non-NCC regos from the 22nd century began with three letters and concluded with a string of numbers... The UE Starfleet of course had no registries in evidence other than NX-01 and NX-02, outside concept art and whatnot, but those two already set quite a precedent before Earth accepts the concept of alien allies.
Still begs the question what NCC actually means.
As far as we can tell, "Starfleet vessel". It's not as if we'd have to believe in other interpretations based on current evidence. Although we can decide to believe NCC on this particular ship meant something else. Or that it meant something else on USS Arbitrary and USS Pickacard but not on others.
Heck, perhaps it meant absolutely nothing on the Bonaventure, but the UFP Starfleet chose to honor this little pathfinder ship by perpetuating its nonsense call letters? They've done stranger things...
Timo Saloniemi