A few thoughts.
Shop around there are watertight hatches designed for decks. Mostly they are aluminum and not fiberglass. Check HamitonMarine.com for hatches. They support the Maine commercial fishing industry which uses more deck hatches than recreational boats.
For large cored areas, plywood of any kind is a poor choice. The problem is bonding to the plywood. Epoxy or polyester resins won't penetrate the hard sections of grain in the plywood. The bonding will be poor which can lead to the fiberglass cracking. Use a foam coring material or use end-grain balsa wood.
Then I would like to dig out the rotten wood between the remaining fiberglass deck layers, fill that area with epoxy and then install two layers of marine plywood on top of the remaining perimeter flange,
I'm not quite understanding the plan here. Without the bottom skin how do you intend to keep the glass and core in place? When you say, "fill the area with epoxy" what do you mean. Epoxy by itself is very brittle and will crack under load. All resins need reinforcement with a fabric and/or thickening material, like talc, milled fibers, colloidal silica.
Leave the bottom skin intact and remove the top skin. dig out the rotten core and clean it up. Sand it with some 80 grit to have a good clean bonding surface. Grind back 3-4 inches on the vertical sides of the cockpit. The gelcoat should be removed and a bit of the first later of glass. Template the core material, spread a thin layer thickened epoxy and press the core material into the thickened epoxy. Once that has cured, then tab in the core material with strips of glass between the floor and the sides. Use at least 2 layers of tabbing. The outer tab should be a little smaller than the inner tab. Wet out the core with neat epoxy and start laying up the glass. When finished you will need to have the glass as thick or a little thicker than the original skin. Now comes the fun part, after removing the pqelply or washing the amine blush off, sand the new glass and begin fairing. It will probably take a couple or more passes with fairing compound to get a good surface. Prime and paint when that's all done.
Once the new floor is in place, decide where you want the hatch. Cut an opening in the floor for the hatch and install. Remember you'll need access to the base of the steering pedestal so it can be reinstalled. Go Sailing.
For more information, WestSystem.com has good technical information. Tech support at TotalBoat.com is good and Andy Miller's YouTube channel Boatworks Today is a treasure chest of information on working with fiberglass.