Actually, RR was spot on.
In these pictures, the rounded outer hull can be seen right at the waterline. The vertical, slab sided structure above this is called the superstructure. The superstructure serves several purposes.
It needs to be remembered that from a purely technical standpoint, the fleet boats were really not true submarines, they were actually submersible surface ships (I hate to admit that, but it is true!
) These boats spent most of their at sea time on the surface and thus their design was optimized for surface operations. The superstructure's primary purpose was to provide a ship-like hull that would efficiently cut through the water while on the surface. It also provided a fairly smooth hydrodynamic fairing around the main ballast tank vents, the access hatches, engine air induction and exhaust piping, and the bow plane operating mechanisms, all of which had to be external to the pressure hull. The superstructure existed entirely outside of the pressure hull and was free flooding. It was always completely full of water when the boat was submerged.
The fleet boats were very large boats in order to provide the necessary fuel bunkerage for long Pacific patrols. Thus, the superstructure was correspondingly large as well. When the boat submerged, it took a while for the superstructure to fill up with water. To expedite this process, holes were made in the sides of this structure so that it would fill up faster. These holes are called limber holes. The pattern, size, and number of these holes were unique to the design to which the boat was built. Some of the earlier fleet boats of the Salmon/Sargo classes were even built without limber holes at all! The superstructure was still free flooding, but it took a little longer.
There were two very similar, but unique designs for the fleet boats. The boats in the photos above are indicative of the design drawn up by the Electric Boat Company of Groton, CT. The large, semi-circular limber holes that are placed right at the bottom edge of the superstructure aft of the bow planes are a feature of the EB design. Boats built at Manitowoc Shipbuilding in Wisconsin used the EB plans and thus they have the same limber hole pattern.
The other design was drawn up by the Portsmouth Naval Shipyard in Kittery, Maine and was also used by Mare Island Naval Shipyard in Vallejo, CA. and Cramp Shipbuilding in Philadelphia. The limber hole pattern consisted of smaller, rectangular holes that ran in two parallel rows. See this photo of Halibut:
http://www.navsource.org/archives/08/0823203.jpg
The roughly 50 second dive times for the as-built design for the fleet boats was more than adequate for peacetime operations. But once the war started, the necessity of making very fast dives became quickly obvious. Getting the superstructure to fill with water faster was one way to quicken dives. Almost immediately refit crews began adding more holes. This was done between patrols and there was no set pattern to it. The original holes remained, but by the end of the war there was an amazing variety to the limber hole patterns as new ones were added.
So, actually all of the photos you posted are correct. They just show Gato class submarines at different points in time.
As the war progressed, there were also several distinct modifications that were done to the Gato class conning tower fairwaters. I have written an article on this subject for my website Pigboats.com. My website partner, Ric Hedman, is busy converting it over to html for posting and when he is finished I will let you know. I think it will answer a lot of questions.