The term you are looking for is reserve buoyancy, and that is the critical term, not freeboard. Freeboard can be thought of as the manifestation of reserve bouyancy in height above waterline, can't it? Look, a submarine sinks but doesn't kill it's crew because it has reserve buoyancy. A vessel can easily be designed to have reserve buoyancy and have decks awash in through the transom all day long as long as there is reserve buoyancy to keep the vessel floating. Even in the story you relate about the Albion 27, the issue was not buoyancy or freeboard, it was maintenance. The owner let a leak go that wasn't designed into the boat, yet he was able to overcome the leak on normal days with the bilge pump. On the day the bilge pump didn't act right, the boat was in trouble, because it lost it's reserve buoyancy. It's reserve buoyancy was lost to excess water in the bilge.
In Coast Guard jargon, vessels don't founder, they lose their reserve buoyancy.
Let me see if I got this right. Are you saying that the only hatch that allowed water in the deck was the engine hatch/cover/bench? There were no other secured or unsecured oval hatches in the deck for access to the lazarette or somewhere else that came loose as the vessel sank? I'm not questioning you, I'm trying to get it right in my head.