The location of the crew rest facilities was made for economic reasons and that is my only point.
Just as a point of interest, the Air Canada 340's have the bunk behind the flightdeck. That means the foward galley is on the other side. It's so noisy there that the pilots were threatening job action to get the bunk moved.
Personally, I don't see the issue with the Captain in the bunk, although I can understand the other side as well. But then I'm came from a situation where the F/Os are trained and trusted.