Great find, I wasn't aware, yet, that we had a quasi-official NCC registry of "1707" for the Intrepid.
First, this has been discussed extensively, I don't believe that the Intrepid
necessarily had to be on the infamous starship status chart in "Court Martial".
IMO, Commodore Stone was well aware of the Intrepid's
repair progress and had simply pulled the starship [upgrade] status chart to notice that Enterprise
) still required upgrades.
In HD it's clearly visible that there is no "1631" on that chart but only an "1831", so Mike Okuda would have done better not to show any Intrepid
Since the whole "1631" registry for the Intrepid has been conjectural from Day One on, add to this that the number didn't exist anymore on the starship status chart once available in HD (becoming even more conjectural), I'd say that the deleted scene and materials outrank this conjecture and should be considered canon, instead.
Second, I believe that the Constellation
had been named and numbered to honor the achievements of a previous ship.
Assuming that in the TOS era they didn't add "A"-ppendixes, shortly after its destruction in "The Immunity Syndrome" a new starship of the 17th design could have been named and numbered to honor the achievements of the Vulcan Intrepid
, that ship was refitted, too, and ended up in Earth Spacedock along with Excelsior.