It is actually 2 3/4" and stops about 25" above the top of the steel floor corrugations. This is in addition to the normal body thickness. I suspect the purpose of this structure is to stiffen the whole body structure. My Sprinter flexes considerably when going over diagonal bumps. Ford addressed this problem with the extra structure and high strength steel. I would think the Transit will be much more rigid structurally and I would not even think about removing any of it. Transit doors also appear to be more substantial than the Sprinter. Sprinter doors rattle.
I will have a cross the back bed located above the 2 3/4" boxes. I will be able to have a bed length of 74" at 32" above the top of the steel corrugated floor. That will be 4" longer than I currently have in my 08 Sprinter where I have to sleep slightly diagonal.