Hmm ... but aren't we now at the starting point again? Correct me if I'm wrong, but the ships in your last scale chart are of the official sizes again, aren't they? And the initial problem was that the Excelsior seems much larger than 467m.
So, the "right" scale for the Excelsior filming model would still be the one that has a deck for each window row on the secondary hull. How high these decks are is a matter of opinion I think, there's only a minimum, as you noted, the 8 ft corridors and rooms a little higher than that, so maybe 9.5 ft is reasonable for that ship.
Regarding the two Enterprises, they are always at the same scale respectively (289/305; 327/344) and their saucer deck heights are the same. They only differ in the height of ther engineering hull decks, and there is also only a minimum deck height to be taken into account here (10 ft, or a little bit more).
(By the way, if your problem is with the different deck heights between the TOS and TMP engineering hull, Nob Akimoto's hull compartments could be a solution. During the refit, they simply replaced the old ones with bigger compartments, resulting in fewer decks.)
To scale the two Enterprises to the Excelsior then, the window sizes (of the TMP Enterprise and the Excelsior) could be a starting point. When the ships are scaled to that, we'll see if it makes any sense (if it adheres to the minimum deck heights).