I’ve experimented with the flaps on my World extensively (probably reported about it on the forum some time ago), and have just like you, experienced a bit of list after heavy rain when flaps and bailers were closed.
I’m afraid the only good solution is
a) find a way to keep your boat on land when left unattended for periods longer than a couple of days, or in bad weather
b) seal permanently transom openings and rely on good bailers only, for better life when sailing and cruising
If you are really interested, I could make a sketch of my ver4 flaps and how they were hinged (these were completely waterproof when closed, but still easily put into [their useless] function). But that would take a bit of time, and in the end, it still all comes to a) and b).
All the best,