There's a lot about Probert's design and original 6-footer that never got utilized in the show. His idea for the saucer edge, the arboretum ceiling, some of the phaser strips, the captain's yacht, and the main shuttlebay*. What was the point of adding the shuttlebay to the design if they only used the ones on the neck? Then there are things that you can't find on the Enterprise model. So the neck has two shuttlebays - what about the cargo bays? Where are they?
*I think the main bay was used twice during the show- Cause and Effect and BOBW Part 2. The interior layout is never seen or known.
Probably came down to budgetary constraints. the Main shuttle bay would have required a huge set which for the amount of use wouldn't have been cost effective.
Add extra smaller shuttlebays to model, build a smaller set (or being able to redress one and money saved.