What about building an already low volume boat with a fairly straight shear such as a CLC Patuxent and lowering the sides. Set up bulkheads similar to their rowing shell at the front and rear of the cockpit opening. Fill the open space with a carved minicell seat unit. You would probably need to put a couple of blocks of minicel together, but you could carve a nice seat complete with legs and foot wells. It would probably be a lot easier than trying to set up a recessed seat that hangs from the deck. You would lose some of the strength that the deck gives you but I think you could get enough strength by adding a few layers of glass on the inside bottom and sided.

John