If I understand you correctly, your bulkheads were never actually water tight as delivered by Amel with open conduit going through? That seems... odd? But boats are odd things...
The water lines do (of course) need to go through the bulkhead to the head sink, and the position of those varies through the production run, but all the ones I have seen were well sealed, and none (of the ones I have seen) were at the outboard edge near the hull.
I haven't seen a majority of SM's by any means, but I have seen a fair number, and that this be a new one for me...
Live and learn...
I'd love to see pictures.