The ST:GEN display has several inaccuracies, such as the placement of the torpedo launchers (we know the forward ones aren't on the deck suggested in the display) and the navigational deflector (which is roughly on decks 22-25 when the movie says deck 15, and
too high up in comparison with the model). And the deck structure shown is somewhat dubious anyway, and not in harmony with most ideas of the size of the Excelsior
But yes, it appears to show nothing but a workbee cargo train in the aft bay, although that bay does have enough room for shuttles, too.
OTOH, it doesn't show a shuttlebay in the ventral cavity, but rather a set of aft torpedo launchers (for which there's no obvious external opening) and then a deck structure that seems to be at odds with the very existence of the cavity.
The shuttlebay that is shown in that MSD appears to lie in the centerline of the ship's saucer and neck, as it is seen extending down below saucer level into what must be the neck. At odds with this necessary centerline placement is the label "Main Shuttle bay P/S", which might suggest that the new add-on boxes are the two halves of that MSB. But the top-down view calls them the "Impulse Reaction System" instead... Too many contradictions to my taste.