Fact: The Making states that saucer separation from the engineering hull was planned as a regular event. Therefore the saucer hull and the engineering hull are two separate identities. The Making states that the saucer has eleven decks and the engineering hull has 16. It states nowhere that the numbering of the saucer continues deck level-wise in the neck section of the engineering hull.
"What do you mean by "regular event"? It certainly wasn't "routine detachable" like the TNG. I assume you mean "standard emergency procedure"?
As for the deck numbering, neither is it stated in TMoST
that the numbering of the saucer doesn't
continue in the neck section of the engineering hull, just because the engineering hull acts as a lifeboat in emergency saucer sep. is no reason to label the decks differently IMHO."
No, I mean "routine detachable". TMoST
explicitly states that there are crew quarters for the engineering personnel of the star-drive (aka warp drive) section in case the saucer has gone elsewhere. There is no need for crew quarters if the only saucer separation is to abandon and disconnect the engineering hull. TMoST
is also specific that the saucer hull contains all the facilities to enable the saucer to function as a lifeboat. There is no suggestion that the engineering hull should serve as a lifeboat, too. After all, most of us expect the onboard elements that could destroy the ship (and make a saucer separation inevitable) to be located in the engineering hull or attached to it.
That the creators envisioned 16 engineering decks is a clear hint, IMHO, that this includes the decks in the neck. If you were to assign deck levels in the neck to the saucer hull, the remaining
16 decks for the engineering hull would have a much lower ceiling than seen in TOS.