David and Jack:
I chose a partial route that seems to work well:
CMC (and VS, too) use the aforementioned "box" on the inside of the bulkhead and surrounding the hinge pieces. It's made of something molded, but not fiberglass - Now that I see the CMC ones from my current kit, it looks like some sort of hardened foam made on a form and shaped into a longish 3-sided box. It's mounted to the passenger side of the bulkhead and the underside of the top of the dash. I had to noodle on it to figure out how it was done (I think Rocky Cimbrec helped, too) and did mine out of fiberglass - they weren't perfectly flat along the mounting surfaces so I buttered the mounting edges up like setting a brick and used Bondo as the adhesive - probably more than I needed, but it completely sealed the trunk off from the passenger compartment. The upside is they don't leak air into the cockpit and the downside is they'll NEVER come out of there. The hinge openings in my trunk are open with nothing over them, but the cavities are painted so they look OK. If I ever get around to putting a trunk liner in there I'll probably dress them off.
On the current build I received the CMC versions of those boxes and they're a bit flatter along the mating edges so I'll just butter them up with silicon caulk and duct tape them in place till cured. Remember that where it mounts to the underside of the top of the dash it's not quite flat, anyway, so you'll need additional sealer.
If you have those boxes and can get under the dash, you could easily seal the edges better with more silicon caulk.
gn