Try a light mix of bleach to water let it sit in bilge while you take a ride then get it out after. Also a nice dose of Simple Green might help. Pop those inspection plates on nice days and let boat breath.
That thin area is there for a reason, so that if water should leak in from drain plug, or other holes (transducers, temp senders) and the seal failed you will not absorb water into the entire transom. actually a very good design feature!