Yes, that's how they come out, which is good as you are now rid of all the old rotted wood.
After sanding and cleaning that lip and 3-ish inches up on the hull, I applied a generous amount of a peanut butter consistency mix of resin and chopped strand to the thin lip. I had glassed my new plywood both top and bottom and simply laid that into the wet "putty" (I had used "bonding" resin on the floor board coverings, but you could sand and acetone wash if it's cured.)
Then I filled the gap between the new floor board and hull side, forming a smooth fillet up the side of the hull about 3/4" inch. Next I tabbed the floor onto the hull sides, with the tabbing starting about 3 or 4 inches in on the floor, smoothly across the fillet, and then 3 -4 inches up the inside of the hull.
I think I've probably got a stronger structure than the original.
Craig Briggs, SN68 Sangaris