I think that when Voyager departed Mars that the Areoshuttle was, for some reason, unavailable. And what the Voyager actually had was basically a "plug," to occupy that space, and make Voyager's underside aerodynamic in case she had to enter a atmosphere.
Alternatively, again the shuttle was missing, and what we were seeing was the sliding hatch/hatches that closed when the shuttle was on a mission, the hatch would make it so the Voyager could land without the shuttle in place.
The intention was to eventually equip the ship with the shuttle.
