My thoughts....
1. Would it be quicker and easier to purchase and install a large ballast bag? When filling, the bag will conform to the shape of the compartment.
2. Essentially, you'll want the interior of the box protected from water as well. So, just because you use marine grade plywood, the interior of the plywood will still need to be protected. That'll be tricky. My first thought would be to cut all your plywood pieces, then fiberglass the interior side of each individual piece. Then assemble and seal the box with the pre-glassed interiors. And finally, fiberglass the entire exterior of the ballast box.
With that said, I'm not sure you'd see any benefits of using actual marine grade plywood since it'll be glassed inside and out. You could probably get away with regular ply, or even MDF for that matter.
Another option would be to cut all your pieces of plywood, and assemble most of the ballast box. Leave off a panel large enough that will allow you access to the interior of the box. Apply an epoxy paint to the entire inside of the box, as well as the interior of the final pieces for assembly. Get the paint everywhere, even as you're attaching the final pieces of the box. You want to make sure the interior is really protected. After final assembly of the box, fiberglass the exterior of it. There are guys that build fish tanks out of plywood, and finishing/protecting the interior of the aquarium with epoxy paint.
As far as needing experience for fiberglassing, don't sweat it. Not a big deal.
2005 Supra Launch 22ssv - yellow/black