sounds like you're a prime candidate for the silicone sealant approach. maybe some others are polyurethane too.

check the archive for more info, but the basic idea is to use a release on one side and spread silicone on the other, mash it down, and when set up a day or two later you have a perfectly conforming seal to any dips an valleys and roughnesses or whatever.

in your case as the lip is so high and you should for sure put the silicone on the lid side. and turn the yak upside down for the day or 2.

so first lower the deck flange lip so you get some clearance for a gasket- say min 1/16inch. then on the inside of this deck lip put clay or cardboard or plasticine or any junk quick filler say flush w/ the lip edge and say only 1/2in or so thick. the idea is that you are making the lip edge 1/2in or so thick and itself lipped so even if the straps fail or loosen the lid has to lift 1/2in or so and is even snapped in place when all fails.

then apply a releas of say sprayglued saran wrap, silicone sealant around this area and mush down the lid. come back in 2 days. you now have a lid with a thin gasket around the flange top area and a 1/2in rough lip that'll snap somewhat(depending on how much you set back the plasicene filler(i'd suggest no more than 1/16in also or flush)

you could even back the upturn a bit, but then make the lip almost flush.
to keep the hatch flush on setup,hot glue some scrap tiny pcs alla round so it wont depress & you can mate it exactly.

some ideas anyway.

-mick