I was wondering the same thing. I went to put the camo skin on my sub and noticed the AI had the camo conning tower. I just thought it was a game glitch and changed all AI boats to have the same skin I got. I am highly looking forward to a fix.
That makes me wonder, are the files on your site, sergbuto, the right ones with the matching conning towers? Would it be safe to use them instead of the ones in harbor traffic mod? Why would docked U-boats have a different file than ones on the move?