I don't see the cost-benefit of taking the double decker out of the back. You gain 1-2 inches, but the expense is way too high what with the replacement parts to cover the gap, new rear cargo mats, etc.
I have not had the chance to use the system. In fact, I have all my tools, tow straps, emergency kit, etc in a heavy duty box in the back that takes up about half of my storage space. So using the deck is impossible unless I go without all my emergency gear.
But I agree with the sentiments. With all the "in ground" features we are seeing in vehicles these days, you would think they could have come up with a way to make the double deck system fit flush with the floor.