So two turntables (elevators)?
That was the possibility I was promoting - as an alternative to the previous idea of placing all the witnessed "Hanger Deck" action on the deck below the shuttlebay miniature set. After all, that's how aircraft carriers are built, too: there's a large surface, the flight deck, for facilitiating launches and recoveries, but the logistics call for multiple lifts that take the craft to and from that surface.
It's indeed quite a mystery why the shuttle takeoff and landing area needs to be that big. But both TOS and especially TOS-R give us hints that shuttlecraft operations aren't particularly precise, and that even a standard launch (as seen in TOS-R "The Galileo Seven") would result in the launching craft badly bruising any other craft housed in the same volume. Perhaps the flight deck is so big because shuttles need a lot of space to decelerate at approach, except in the most sedate of situations? Or because there's something analogous to "wind" to complicate flight deck approaches - say, the unpredictable relative movement of the craft and the mothership?
It's also possible the deck is big simply because it is designed to accept larger auxiliaries on occasion. Say, the gigantic aquashuttle from TAS "Ambergris Element" wouldn't fit aboard at all if the shuttlebay was only sized for economic operation of the Class F craft. And some other auxiliaries or visiting craft may be larger still.
On the two-lift idea, note how the TMP-refitted ship has elevator surfaces (square, paired, non-rotating) roughly where this putative second turntable would be. Hell, there might be three elevators in TOS already: one central, close to the aft doors, and two farther forward, possibly larger and non-rotating just like in TMP.
Another idea would be having two lifts/garages side by side at the front end of the flight deck, behind rolling doors. The ST5:TFF set suggests this. In TMP, the garage doors and walls might have been removed, but the actual volume would still be allocated that way. Or the doors and walls might be present even in TMP, but would be moveable, just like some other walls in the secondary hull are shown to be moveable in that movie. Perhaps the differences between TOS, TMP and TFF are actually rather minimal?