When you place boat underwater in most cases its placed above your head and emerges. You can sit on it and emerge too.
But on low altitude, underwater, boat is placed on ground and start sinking into solid blocks and dissapear until you destoy some blocks of the ground and see it again. When you place boat and get on it you will sink into solid block too. Sometimes when boat is inside ground under you, image is shaking and you cant move until you destroy the boat.