Removing the 3rd row seat is not a big deal. There is a single bolt at the bottom of each of the 8 legs, and the seats come out separately and are light-weight.
Yes, there is a considerable amount of space in that spot (because of the increasing depth as you move forward, almost 3 times the space of the storage compartment). If you take long trips often, its a great place to hide a wide assortment of emergency equipment, spare fuel (in the "safe to store-in-car formula"), folding shovel, snow cables, etc.
I would purchase an extra storage lid and plastic hinge receiver (brace yourself for the $154 + $28 retail price), and build a false frame out of 1" lacquer sealed pine board. This way, the custom modification will look completely factory matched. Otherwise, you can build your own deck and cover it with automotive carpeting, as best as you can match it - just don't expect a perfect color match. Automotive upolstery places might have a larger assortment of carpet than your local auto parts store.
Good luck.