Mike, a quick check shows that at least one volume on the Union Navy, Donald L. Canney's LINCOLN'S NAVY, shows the differences between Naval Yards and Stations, and other facilities. Mound City is shown, in official publications (the one I checked being the NAVY REGISTER for 1865, printed by the Government Printing Office, Washington), as being a Naval Station. In 1865. there were only eight Navy Yards (Portsmouth, N.H., Boston, New York, Philadelphia, Washington, Norfolk, Pensacola and San Francisco) and three Naval Stations - Baltimore, Mound City and Memphis. Then there were the Naval Rendezvous and Naval Hospitals. Canney indicates that the Navy Yards were the largest facilities, followed by the Stations and so on, down. If anyone has listed Mound City as a Naval Yard, then they are obviously in error, or clueless about these facilities.
The photo I have of the Mound City station, is a different one from that in the IOW, and shows three officers (instead of two) standing on the planks. It was purchased some years ago from the Samuel Massa Collection, in the Syracuse University Library. I purchased it together with four other Naval photographs, all of which, I believe, have not been published elsewhere. See my link below for two of these photos, of Massa and his fellow warrant officers.
I have xerox copies of numerous articles from various Civil War newspapers, including much from the Chicago Tribune. I will check to see if I can find anything on Mound City, and let you know if I come across anything.