Do starships have arboretums/ae/whatever in the usual case? We have only ever heard of the TOS and TNG Enterprises
The shuttlebay-like thing at the extreme stern of the Excelsiors
is also used as a ventral detail at the stern of the Ambassador
class (the later appearances of it anyway), in close proximity to another blatant stern shuttlebay. Could be that a bay of this size and shape is specifically intended for cargo loading and offloading, with the help of those workbee-towed container trains we see in the movie era. And the "real" shuttlebay of an Excelsior
might then be elsewhere, possibly in the ventral cavity discussed above.