Hi Brian:

I'm not one into big debates over hypothetical things.

If it was my boat, I would use that stuff or maybe yoga mat material. Bolts in every indentation on the flange with a wood ring under it that I would coat with epoxy for waterproofing. Large fender washers under the nuts. It needs a cushion under it and the stuff I have doesn't tear easily and is waterproof plus it will be under compression compensating for any differences in the flat planes of the boat and bottom of the hatch base. A wood ring under the boat would stiffen it so it doesn't bend under load.

Don't forget, the automotive industry used paper and cardboard gaskets on engines for a lot of years and under compression they were waterproof and heat proof. They were just impregnated with oil. Any rubbery material would work as long as it's not too thin so it compresses and fills out any inconsistencies between the two planes.

If you look around in a hobby shop or craft shop you might find a perfect material.