The hatch lids, when closed, are supported from below by the gutter on three sides, no? All the front latch needs to do is keep the lid from flying up. So, instead of latches so big and problematically deep, why not put a small twist or slide latch fully within the 1" thick hatch? Much like an ordinary door's hardware pops out the edge of the door itself. But with a flush-mounted slide or twist on the top of the hatch lid to engage/disengage it? Could be MUCH smaller than the big ones in the pizza mockup, allowing the whole thing to fit within the 1" thickness you have to work with.
On protecting the gel when using the seats: couldn't you make any sort of cushioned support for the seatback/hatch lids down below the level of the deck? Say, imagine the rain gutter going around all 4 sides, with the aft side having a friendly, non-marking cushioned strip along its front side, fitted to the curve of the hatch lid. Cut two notches in the aft portion of the sides of the gutter, for the sear backs to slide up and down. Done. Further, with the hinges you have, and the right notching, you might not even need a latch on the bow end of the hatches. Instead, just a fixed pin and slot, so the forward end was captive while the hatch was closed. Assuming changing configurations means pulling the hinge pins anyway, the hatch lid will be completely free during the switchover. Pull it up and out, lay it close to flat, slide the bow end into place with the fixed pin going into its slot, drop the stern end in place, replace the hinge pins.
For a totally rattle-free fit, you could even file a tiny hint of angle on the pin. And/or use two pins per hatch lid.
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Simple, no obtrusive, clunky hardware to sweat when using the seats.
Just some ideas...
"I don't have time to get into it, but he went through a lot." -Pulp Fiction