if there is any common sense to the design of the ship i would say the hanger on the bottom of the ships belly behind the deflector was left intentionally empty to support mission specific hardware given starfleets history with modular design
I can't recall exactly where I read it, I think it was a blueprint pack of the Excel, but it's original purpose was exploration and support. If I remember, the huge open spaces were to hold/integrate mission modules like science equipment, and colonial modules like terraforming gear and prefab enclosed colony habitat stuff.
That all seems to fit with the time period it was designed in. Fed was still expanding, most worlds weren't fully habitable yet etc.