Star Wars

Disclaimer: Deep background reasons are usually written or fleshed out after the prop has been made.

There is just no way this provides any kind of advantage or is necessitated by some design constraint. In fact, they could just rotate the cockpit gondola until the body is underneath or above.

The did! The ship's cockpit is in a rotating gyro mount. When the B-wings started their attack in ROTJ the cockpits were positioned on top of the ship.

The shorter s-foil wings stay flat on the body while not in attack mode and then fold into the cross shape for combat. The entire logic behind folding s-foil wings has been debated to death by nerds since the existence of X-Wings, but let's just assume there is a rational reason for the folding and unfolding. With the wings folded flat, there isn't a great spot to put the cockpit on the longer portion, and then the engines and big cooling system being near the center makes sense to me.

The Star Wars Essential Guide To Vehicles And Vessels does say that B-Wings are notoriously difficult to pilot, but that pilots who got good with them became very attached. The book also says that the gyro system for the cockpit allows the ship to do a lot of crazy maneuvers with it rotating around while not putting physical strain on the pilots, since the cockpit stays in place.