Oh, you're asking about using aluminum plate to replace the cut out deck....
Hmmm, I guess why not? How big an area? You may be able to use thinner than 1/4" if the span isn't too wide.
Or you can just mod the fiberglass you cut out (Cut carefully) with an Aluminum or fiberglass flat bar lip all around and bolt it back in.
Untreated aluminum plate will start turning things like your knee etc you put on it grey from the surface oxide residue. If you are in the salt water
it will get fairly ugly compared with the fiberglass.