In the case of this particular warping issue, depending on the amount of distortion, I would consider just using a thicker, maybe softer, gasket.

If I ever do a ply deck again, especially a curved deck (which I don't think this one is), I will make the hatch lids using strips, by putting down plastic and using the deck as a former for the lids.

I would cut the holes first, and put in the lips, as the process may cause the deck radius to change slightly in the hatch areas, then glue up the strip lids.

Ply lids on curved decks never really perfectly mirror the curve of the deck, especially since I don't glass ply decks.

It would also add a little decoration, especially if one stripped the coaming ring as well.

Of course, this is not an issue with chined decks.

Et.