Digging into some terminology from "The Cage" and taking a closer look at screenshots from TAS, it may be possible to rectify TOS registries with classes of ship. Here's the short version, more details below: The Bonaventure's real canon registry could be 1028, and it was an early faster-than-light "hyperdrive" ship, converted to "warp drive," while later ships were true "warp drive" ships.
Here comes the reasoning
The Bonaventure from TAS is listed as having the registry 10281NCC. This seems too high. BUT...as would be correct for that time, and just as the Enterprise had in "The Cage, the number "1" and the letter "i" were represented by the same character. Meaning it really says "1028 i NCC" or "i 0281 NCC or "i 028 i NCC"
Let's ignore the use of the term "warp drive" in 2001's "Enterprise" for the moment. In "The Cage," the term "hyperdrive" is used, but Tyler speaks of a "time" barrier being broken. Perhaps, in its day, "hyperdrive" was a slower, but still faster than light, version of warp drive, and still the term used in shipboard commands, while the Enterprise had a true "warp drive," breaking the "time" barrier.
Scotty of all people, should know what he means when he says the Bonaventure was the "first ship to have warp drive installed." Perhaps this ship belongs to the same class as the Constellation NCC-1017, and maybe even the Eagle NCC-956. These ships had slower "hyperdrive," and while not the oldest, Bonaventure was the first to be a testbed for installing the faster "warp drive." Constellation and Eagle were later refitted to appear like Constitutions.
I have a TV guide from 2001 in which Berman and Braga say that they decided not use UESPA on "Enterprise" because it was unfamiliar to audiences, and that they used "warp drive" instead of "hyperdrive" because they felt it was a generic term that they would not trademark. I can't find it now, so I can't give the exact issue. So the terminology used in "Enterprise" is not able to disprove this theory.
Consequences of this thinking:
Maybe that is also why ships like Exeter and Excallibur have lower registries than 1700. They were also older designs refit to Constitution spec.
Maybe the reason no one trusted the Excelsior at first was that it was the first true redesign of starships. A Bonaventure-type could by updated to a TOS-style; a TOS-style to a TMP-style, but Excelsior might have been a totally new platform with almost no structural or functional relationship to older ships. I think that makes a ton of sense.
Here comes the reasoning

The Bonaventure from TAS is listed as having the registry 10281NCC. This seems too high. BUT...as would be correct for that time, and just as the Enterprise had in "The Cage, the number "1" and the letter "i" were represented by the same character. Meaning it really says "1028 i NCC" or "i 0281 NCC or "i 028 i NCC"
Let's ignore the use of the term "warp drive" in 2001's "Enterprise" for the moment. In "The Cage," the term "hyperdrive" is used, but Tyler speaks of a "time" barrier being broken. Perhaps, in its day, "hyperdrive" was a slower, but still faster than light, version of warp drive, and still the term used in shipboard commands, while the Enterprise had a true "warp drive," breaking the "time" barrier.
Scotty of all people, should know what he means when he says the Bonaventure was the "first ship to have warp drive installed." Perhaps this ship belongs to the same class as the Constellation NCC-1017, and maybe even the Eagle NCC-956. These ships had slower "hyperdrive," and while not the oldest, Bonaventure was the first to be a testbed for installing the faster "warp drive." Constellation and Eagle were later refitted to appear like Constitutions.
I have a TV guide from 2001 in which Berman and Braga say that they decided not use UESPA on "Enterprise" because it was unfamiliar to audiences, and that they used "warp drive" instead of "hyperdrive" because they felt it was a generic term that they would not trademark. I can't find it now, so I can't give the exact issue. So the terminology used in "Enterprise" is not able to disprove this theory.
Consequences of this thinking:
Maybe that is also why ships like Exeter and Excallibur have lower registries than 1700. They were also older designs refit to Constitution spec.
Maybe the reason no one trusted the Excelsior at first was that it was the first true redesign of starships. A Bonaventure-type could by updated to a TOS-style; a TOS-style to a TMP-style, but Excelsior might have been a totally new platform with almost no structural or functional relationship to older ships. I think that makes a ton of sense.