Yes, that's correct. The scuppers stick out into the cockpit. I'm not actually sure what happens to the ball when the cockpit floods - I assume it is forced into the hole, keeping water from flowing through the hole into the cuddy. But if the cuddy gets water, the ball moves away from the hole and lets the water drain into the cockpit and down to the self bailer.
My boat is moored about 30 minutes from home, or I'd get a few pics. If my boat didn't have them, I can't really say that I'd be anxious to add them - they look sort of clunky, but I suppose they work as intended.
I'll have to try to dunk a rail next time I'm out to test out the set up. Or not.
