I've toyed with the idea of fabricating parts using the molding process, but all the parts I make are one-offs. If you were to go commercial with your trunk, a "master" mold would be the way to go.
What has worked well for me, for the bodywork I have made, is to form the rough outline of the piece using light gauge aluminum sheet metal ( such as roll stock, used for trimming around windows and doors), then obtaining the final shape with body fill, then a layer of fiberglass, finally finishing like you would a car panel. Very durable results. I've never had anything crack with mileage.
Important that the bodyfill layer is used, since fiberglass does not bond as well to bare metal.
A foam and vinyl covered seat trunk would not require an exacting final shape or finish, for obvious reasons.
Using the existing seat mounting holes for the trunk would be the simplest and best solution. Easy on, easy off.
Your idea is such a good one that I'd make one for myself, but the area under my rear seat is always occupied by one of the two auxilary gas tanks I use, dependant on the mode of the bike - street use or touring.
Cheers!