How do you get them to sit flush? Thanks for the advice.

The hatch cover and deck must first be shaped on the same plains and curves. This may require removing the hatch cover interior glass with a heat gun to make the hatch cover flexible once again. I've done this and then hot glued shaped 2x stock to the exterior to hold the hatch cover in the correct shape while adding a new layer of interior glass.

Shock cord will never apply enough pressure to seal a broad gasket making it waterproof. The broader and thicker the gasket the more pressure needed to seal it. The flatter the deck the less downward pressure shock cord will apply. Levers and other mechanisms will be only slightly better.

If you use spacers under the deck lip to make-up for the gasket thickness, with a gasket in the sandwich, how thick must your spacers be? The gasket at full thickness or compressed? How much will it compress?

The key is using rare earth magnets and a gasket inside the spacer so the gasket has room to be compressed without being flattened. This arrangement allows the magnets to contact, their strongest position and doesn't try to compress a broad gasket flat. The hatch cover can lay flush because you know how thick the hatch cover will be relative to the deck lip.

The bead makes a positive impression into the gasket making the seal waterproof.

This system has worked simply and reliably for me for years.

Rob