Capt:
I don't like E-Track on the floor, but many others do like it there. It's always dirty in the slots and I'd worry about an errant skid nail or the broken leg of a 1500# metal tub fetching up in on of the slots too far forwad for a towmotor to reach.
If you must, consider 1/2 inch plywood; you'll need the extra 1/4 inch height quite often to get a 4' tall skid in the rear opening. Another reason for the 1/2 inch ply is the E-track thickness is 1/2 inch so between the track and ply you'll have a flush floor. I'm not sure how the majority fastens the track to the floor but I'd use either construction or silicone adhesive to secure the plywood.
For what it's worth, I use Baltic Birch plywood. It comes in 5x10' sheets so I cut them to contour with the wheel wells and outer van walls. It can't slide fore or aft when installed this way. Whatever type of wood you use, coat the surface with a waterbased urethane so it won't absorb oil and dirt and can be wiped clean rather easily.