thoughts only:

clc has a forced curve deck. when a hatch sized opening is cut the sheer side central edges of the hatch opening will tend to open up a bit. the hatch cutout (even if curvature is maintained) will have less curvature on these same edges as its a bitch to keep curvature going to a finished edge/end in any curving situations. bitter lesson learned in another application.

in order to preserve the curvature in BOTH, why not put the double layer in before cutting the hatch out, and stitch and glue it in place along the hatch cut out line. remove the stitches later and cut both out at once. is this impossible to do? if not the curvature changes in both will be minimized. if it is impossible to do, can you refit the lower pc in the opening(as its ellipticalish) and s&g thru the previously marked (on the lower) and cut out top. cinch like hell, then cut out.

if you want to relieve hatch somewhat, do it in lines across the yak so that stiffeners will remain, but leave the edge as is.

then off set the lower lip by say another 1/8 spacer, and say make it 1/2in less all around in size. use the braced silicone or urethane approach but make the gasket(in the hatch side) 3/4in wide and mush down upside down yak so the sealant wont move too much. you want the sealant to gush up the inside edge.(i'd mask the inside say 1/32in back or so)

pop it off if you can(hehe) and you will have a perfect mating surface as well as a slight jammer to say 1/4 in of movement up and down(dependingh on how much mushed up). you may have to trim excessive overcuts a little bit. i think the best would be if it just snapped in place over say 1/4in of downward movement. will help to keep in place even if latch failure.

-mick