Yeah, besides Stone's wall chart, there's also the Republic NCC-1371 mentioned in Court Martial.
True enough. But that would again be a "bygone" ship. If the range of registries for currently operational ships is as narrow as indicated in TOS, it's tempting to deduce that lower registries eventually disappear from use, and that there has been a steady progression from NCC-1 to NCC-1887 in the century or so that Starfleet has existed, and finally that we can then reverse-calculate the lifespan of a ship class from this data...
It is only TOS-R that sort of challenges this, and even there it could be argued that the low-registry transports we see have every right to be really ancient - especially the ones that have been automated for ore hauling duties.
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.
I think it's only beneficial to continuity that there would exist the separate starship Defiance
that was in no way related to the ship that went missing in "Tholian Web". But as said, the Defiance
is not among those elements of the old Tech Manual that would have gained canon status.