I pulled my rudder box on my 06 x9 tonight. It was sealed with Silicone as well. I am actually very happy they didnt use 5200 on it as it makes it significantly harder to remove. I would suggest 4200 as it is removable on a part - such as a rudder box with could require removal for repair or rebuilding after time.
BUT - I agree with your point. A 2 year old boat shouldnt leak.