There are other ways, but I think the wood is as good a way as any, and the Trillium
is already set up for it. I think they originally used plywood, but I have heard of people using other rot-resistent wood as well. If you want to have it show, then I would use something nice looking and varnish or paint
it tidily (originally, the Trilliums I've seen have the wood under the Ensolite, and taper the outer edge of the wood at an angle so the Ensolite can "ride up" a gentle slope).
Although stainless screws are not rust-proof, they are rust resistant at least. Since you are in Florida (and will perhaps be near salt water), I might isolate the stainless from the aluminum with a bit of Tef Gel or similar, although if you don't it will still probably last another decade or more.
Butyl is a good choice for sealing. I would clean the surfaces (window and fiberglass) well with denatured alcohol or acetone before reinstalling.