forget pin holes, for now, just think about when you move hose reels in and out or other items in and out of van this paint is not as hard as steel it wears quick if stuf is moved about on it a lot. this will cut through the paint and water will get in at least if there is no ply you will see the problem so can be sorted, leave ply in and it will soak it like a sponge and then the water will want to get out and the way to do this is down
When you drag things in and out I believe you will see if the ply is damaged as well as it is soft so it will mark ( I have had my van for about 3 months no damage to ply yet ) , so you can touch up the paint. Not only that you should be using marine ply wood, which is waterproof, If you maintain your van properly like me, you would see any marks to floor or damage on sealing, so nothing will leak through underneath.
To me it looks you can do the protecta-cote both ways, on the ply or take out the ply, it just means you will have to keep eye on covered areas and maintain floor if its damaged which ever way you do it.......