It's not as if the idea of two dissimilar bays, one atop the other, would be particularly bad or even unprecedented. The "upgraded" Ambassadors
have a clamshell-door bay at upper stern, but also another bay at lower stern - and upside-down Excelsior
bay in fact. There might be merit to having a separate bay for the workbee trains or lighters that bring consumables aboard, so that the tactical or scientific errands of the shuttlecraft aren't inconvenienced or vice versa.