I bought my first pontoon years ago the guy had re-decked and laid new carpet. It was regular pressure treated plywood and it lasted a while but had soft spots in it and then became dangerous within 5-7 years. With that said I think any kind of treatment would have been better than nothing. When I re-decked one a few years ago I used some polyurethane coating from Sherwin Williams on marine plywood that was super tough and cost around $100 per gallon. It was hard when it dried but flexible enough to move with the boat.
In other applications, I've used BEAR concrete paint on plywood benches in a shop and it's super durable. The cost is $25-30 per gallon.
I get what you are doing with the boat and not wanting to spend the money on the high priced marine plywood, so personally I would use a couple or three coats of the concrete paint for a tough coating. You may not get anyone at the home stores that will support the idea of using it on wood but I've been using it regularly on wood for at least 15 years. I would use it instead of the water seal products made for decks. Just my 2 cents.
