There is a guy in NSW, Australia who has done some nice fiberglass work on his kayak. He made a fiberglass insert for the tank well on his Scupper Pro that is similar to what you are looking for.
http://www.akff.net/forum/viewtopic.php?t=6415
http://www.akff.net/forum/viewtopic.php?t=6286
You could easily put a hatch cover on the bait tank of this type of set-up.
He also did a fishing ski-style fiberglass center hatch for the Scupper Pro that is a thing of beauty.
http://www.akff.net/forum/viewtopic.php?t=7658