I wasn't doing a Wagon, but working on my Runabout when I decided that the carpet needed to go from the rear of the car. The hatch had been leaking for sometime and the carpet in the back was shot. I gutted out the interior from the rear half of the car, including the rear seat and all the panels. At that point I threw out the old carpet and basically went over all the exposed metal I could with a scotch brite scrubby. I had already done the same to the underside of the car and sprayed it with the Rubberized Undercoating available in the spray can a while back to try and get a grip on some rust areas.
At that point I shot more of the same rubberized coating into all the open areas of the body panels I could get to with all the panels out. I also used some plasticized filler material to plug a few small areas where the leaking had been coming in. I also took the time to shoot all the rust spots with some etching primer after loosening all the damaged material I could take out, before spraying the coating material.
I did what I could to reuse or replace any insulation that had been damaged or showed signs of either mildew or previous water damage. So then I was ready to roll out a coating of truck bedliner coating material. It took two coats for decent coverage and a few days to fully cure. The product I used was, I believe, Hercu-Liner. It was easy to roll onto all the exposed metal. The gallon kit I bought for about $80-90 if memory serves me. The gallon kit had enough of the coating to do the inner back fender wells, the "trunk" area including the metal under the interior panels, the metal back plates for the rear seat and the bottom of the seat wells under the rear seat, and I still have enough left to do the floor in the front of the car if I get around to it shortly.
I need to redo the upholstery in the car, but at the time I only did some replacement panels on the rear seat so I chose that as my stopping point at this time. I've found several suppliers for the preformed carpet for the front of the car, but I'm somewhat financially embarrassed at the moment and not able to afford to do too much work right now. I've seen rockauto.com has the carpet and floor mats in multiple weights available. You might check them out just to see the specs.
I think that once I finish out the floor in this bed material I'll definitely want to add the carpet back, but I've found that the liner stops rust pretty well, it seals up the metal and leaves a very rough texture that took the spray web adhesive I used very well and bonded nicely. I think the surface will be perfect for making sure the eventual replacement pad and carpet stay where I put it. That being said, the rough texture is created by using a rough textured roller that there's two of in the kit, but I think it could be laid in smoother with a different roller if you wanted.
More importantly to me right now though, the texture stops things from sliding around too much and I've found it to be alright to live with in most other ways. It does insulate and deaden sound to a degree, but isn't an answer in and of itself, just a component to add a little bit more. I only did the two coats by the directions, but I feel like you could layer it up a bit thicker if you wanted to add a bit more thickness.
Unless you just have access to some other materials to work with, I think the liner kit ends up being a good deal. You get a tough durable surface to protect the metal that looks pretty good to me. (They had a couple of tinted options available, but I did mine in black.) It'll be good under the carpet later, but doesn't need to be babied in the mean time. I just haven't seen any downside yet. I think its a good intermediate step for everyone and it'll be a finished product for a lot of people.
That's the direction I'm going in anyway, and thought it sounded like it might belong in the back of a wagon like yours.