The reason for the three section deck has to do with the original Aurora release of this kit.
Aurora offered a motorizing kit for the original USS Enterprise and the center deck section allowed access to the battery compartment. As I recall, the original center deck section was held in place with a tongue and a tiny screw. A few of the motorizing components were included with the Enterprise kit and rest were in a separate motorizing kit included two electric motors (duh) and might have also included the battery box (4 or 6 "C" cells), mounting brackets and worm gears for driving the screws, and the associated wiring and electrical hardware. There was a sliding switch mounted somewhere on the hull side toward the rear to turn the motors on and off.
I waited weeks for the local hobby shop to get one of the kits for me which gave me time to save up the princely sum of $2.00 to purchase it back in 1968. I got the hardware all mounted and ready to go and filled up the bathtub. I could hardly stand the anticipation of watching CVN-65 on its maiden cruise so I turned on the switch and to my huge disappointment, the thing barely moved! I guess the screws were just not big enough in this scale to provide much thrust.
Martin