Hello John,
I've seen this model in person some time ago and noted the same differences. At that time a Porter family descendant in Portsmouth allowed me to see the original Virginia plan as done by J. L. Porter. It shows these 'decks' fore and aft. He desired to sell it to the Smithsonian Institution but a relative had already sold them a copy and they did wish to pay the asking price. Eventually the plan was sold just a few years ago.
Anyway, the Virginia was an experiment. There were two competing designs of similar concept by Brooke and Porter. Mallory chose Brooke's concept and asked Porter to work out the design details and construct it. If you recall from Brooke's initial draft it called for water tanks to be placed fore and aft of the casemate. These would be emptied in normal service and allow smoother handling and steaming. In battle, they were to be filled with water lowering them beneath the waterline such that only the casemate appeared above.
Porter had a problem. He had to make this concept fit on a pre-existing hull of deep draft. He appreciated only having the casemate exposed in battle, but how would he do this on the Merrimac hull? Despite his best efforts to cut down the hull, she remained deep draft and heavy by the stern. The fore water tanks were not ready in time for Buchannan to act. This deck and the planned aft one would have given space to handle her anchors and mooring gear. To bring the bow down and level the vessel, pig iron was placed within a wooden breakwater on the bow as an interim measure. This would later be planked over to allow crew movement. As the stern was already beneath the water, no tanks, weight or breakwater with deck was placed there. There was a connecting deck to support the upper pinion of the rudder but that was all. It remained a very vulnerable part of the Virginia.
The model reflects Porter's original draft with Brooke tank decks fitted fore and aft. Other details, such as boat arrangements are hypothetical. It does not reflect the Virginia 'as fitted'. That is my understanding of the model. It is a beautiful piece of craftsmanship.
All the best,
Bil