Our 1978 Trillium
4500 has similar issues where the interior fiberglass components the comprise the floor don't lay flat. In our case either a previous owner or the manufacturer put some screws through the fiberglass floor into the plywood. To install finish flooring, I would have to remove the screws and somehow secure the fiberglass flat to the plywood. I would probably use construction adhesive and hold in place with some heavy weights, e.g., sandbags.
Edit: On our FG floor, there is also a 1/2" gap between 2 interior FG modules (i.e., the plywood is exposed here). I would probably grind the edges here and fill with bondo-glass.