I think most RV toilets have a flat toilet flange and a rubber seal. The bottom of the flange is on top of the plywood. If you change the floor height, you may have to pull the existing flange up. Mine is glued to a 3" pipe that slides into the black tank. A lipped gasket seals the tank to the pipe. I know some have a 90 elbow beneath the toilet and the black tank entry is offset.
Is there any possibility to remove the bad floor and replace, maintaining the original height?