Based upon my own personal hands on experience with the OEM mat and its ravages of humidity saturation on van floors......
You're on the right track with the coating. I used POR-15 silver because surface rust on my "new" 2003 was sufficient to warrant that treatment. I also treated the front floor boards as they too were rusted although a bit more than the rear area. POR-15's formulation gives me supreme confidence existing rust will be mitigated or stopped dead, the resulting coating adhering to the sheet metal more tenaciously than the original paint finish.
In the rear area I cut sheets of AB plywood, 3/4" thick. This was laid directly on the floor, naturally it rested on top of the ribs in the rear floor. No screws used that penetrated the sheet metal at all, instead I ran the plywood under the lowest flange of the sidewalls located just above the floor. Strips of poplar or similar were fitted between the plywood sheet and the flange, screws used only to secure the strips to the flange. This arrangement somewhat "wedges" the plywood to the van floor---it can't move.
Joints in the plywood were addressed by cutting the pieces so a seam would exist directly above the space formed by the floor sheet metal ribs. Because that space was 1/2" in depth plywood strips 1" to 1 1/4" wide were fitted into the space, wood screws countersunk through the plywood floor into the 1/2" strips as a way to hold the seam together. (Had I been more motivated I'd have cut 1 1/2" lap joints in the plywood floor plus used the 1/2" plywood strips underneath the seam----this would been a very strong joint/seam without need to screw into the floor metal.
This method of leaving air channels under the floor is best. There is no need for sound deadening material or anything else under the plywood of the van floor. Once carpet or other floor covering is in place layer upon layer of FatMat etc or insulation is time and money wasted.
Keep in mind Ohio weather covers all four seasons with frequent dew and condensation which absolutely kills a bare uninsulated van with the OEM padded floor mat. Other climates might not be prone to issue but the flooring system I describe is just as effective regardless.
Anyway hope to see more of your progress!
PS: Have to edit this now---new reply from Evy!
As long as the OEM padded mat never again comes in direct contact with the van's sheet metal you're good---its a rather durable and well-made mat overall. The coating material you're using should work to that end.