OP said: I plan on some sort of rolled on product instead of carpet.
Yes Rich, I am assuming the transom, deck or floor panels would be painted after preservation.
paint and varnish does not adhere well to silicone or siliconized caulk.
Thus my strong recommendation of the silicone-free Alex or PolySeamSeal caulk on anything that
will be coated down the line. This is for any household projects as well.
if the end result will be varnished natural wood, then Like Dale says,
epoxy the end grain. It will cure somewhat clear and give very adequate protection.
When making MDO sign panels, I used the method as described above using the caulk filler.
after the caulk is applied, you can smooth it down with your finger and when it cures, prime
and paint as you normally would. you can not tell it is plywood . . .
these two signs are examples of 3/4" MDO plywood..... they are meant to last for many years.
proper preservation and the correct primer and paint gives the customer assurance that they will.
I know this seems like a far stretch from boat decks, floors and transoms. But, the procedure of
preserving, priming and painting plywood is basically the same, regardless of how the end product
is used.