Epoxy resin makes a very good adhesive even when used without the fiberglass, albiet a tad expensive. If instead you have a polyester based resin, it is not as good as an adhesive. Be sure to confirm which you have. If you have epoxy resin (not polyester resin) and you think you have enough, I would use it to glue whatever is needed.
Regretfully, I cannot envision what was done with the 6" squares in 1/2" and 5/16" ply, as my Seafarer floors are all fiberglass, so I can't comment specifically on that part. Generally, I see no reason to use multiple small pieces of plywood, if a larger piece is available instead. While this may not be relevant but for what it is worth, given that epoxy works so well as an adhesive it can be used to make multiple pieces of ply into one, or laminate thin pieces into one thick one.
What year is your Seafarer? I am wondering if possibly the ply pieces were added by a previous owner to firm up flexing in a fiberglass floor. As noted earlier, my Seafarer floor over the tank is made of all glass, no ply, but I have noticed that one of the ribs in the floor did not get saturated with enough resin during production and has, over the years, started to flex a bit more than it should. If that same thing happened in yours, perhaps a previous owner added the ply to try to repair a similar weakness (which may or may not serve well in that manner). Just a thought.
BTW, we love Callao. Although we are down in Lancaster Co now, we spent several years at the Yeocomico Marina in the late '80s and early '90s, which as you probably know, then became Port Kinsale.