After my post last night, I decided to see what happened if I scaled the engineering decks to 12 feet (including the between-deck spaces.) I found that this resulted in an overall length for the refit very close to the official 305 meters. ...
For me it looks like only the Refit has different deck heights in the saucer and engineering sections. The TOS version has (approximately) the same deck heights throughout the whole ship.
I wonder, if on the TMP ship the engineering section decks are 12 ft high, would the saucer decks be around 10 ft? If yes, then the saucers of the two ships would align (as they're supposed to as far as I know) and we would be back at the official sizes for both ships. I would then scale them up again to 327m/344m because of some things which fit better at that size of the TOS ship (In the thread I posted a link to in my last post Cary L. Brown came to his preferred length of 1067 ft because of this. If I remember correctly the shuttlebay would fit behind the nacelle pylons, the bridge would line up better with the dome and the turboshaft "knob" and there were a few other things I think).
With the 327m/344m scale, the TOS ship should have decks around 11.3 ft high and the TMP ship saucer decks of the same height and engineering decks of around 13.6 ft.
Then, you could try to scale the two ships to the Excelsior based on the window sizes, although of course the space between the window rows is a factor too. Well, as you said, it could be intersting... or utterly disappointing. ^^