Re: Adding woodwork below
That wheel has already been invented and we probably won't come up with a better solution here.
Get Casey's book. According to him, as I recall, boatbuilders use a flexible foam spline--a strip maybe 1/2" thick and a little wider than the thickness of the plywood, beveled at the sides--between the edge of the plywood bulkhead from the cabintop. That lessens the problem of creating a hard spot under your deck. They then layer strips of fiberglass to bond the vertical board to the cabintop. Look at the way original bulkheads on your boat are attached.
Alternatively, would simply raising the height of the partition to an inch or so short of the cabintop meet your needs? That would be much easier structurally.