Very true. Mitsubishi had two armaments plants at Ohashi. Morimachi and Mitsubishi both had steel plants located in the Urakami Valley, away from the downtown area of Nagasaki. Those targets were detroyed and the residential and business districts of Nagasaki were spared due to the topography of the area.
Bock's Car made three bombing runs on Kokura before Sweeney made the decision to head for the secondary target, Nagasaki. Smoke from the fires still burning from the previous nights bombing of Yawata, by 224 B-29s, prevented the drop on Kokura. Wonder how Stimson was able to manipulate the surface winds to accomplish that feat! One of the many points that revisionists gloss over is this: In the three months that Truman had been President, the United States sustained almost 50% of its total casualties in the Pacific Theater.
On paper it may have appeared that Japan was defeated, but such was not the case. The Japanese conditionally accepted the Potsdam Declaration on 10 August with the following major caveats: Japan would try its own war criminals, Japan would retain control of its troops and disarm said troops itself, the Allies could not occupy the home islands of Japan, Hirohito would remain sovereign ruler. The Allies rejected those terms. Truman counter offered that Hirohito could stay but under the authority of the supreme Allied commander. The Japanese did not reply but instructed their forces to fight on. The Allies toned down their offensive actions and began dropping surrender leaflets instead of bombs. Finally with still no response from Japan, Truman ordered Marshall to resume air raids against Japan. On the 14th Spaatz ordered anything that could carry bombs into the air. The result was the largest raid of the war; 2000 airplanes bombed Japan. High ranking officers planned a coup after Hirohito told them he would announce the surrender to the Japanese people over radio. The coup attempt failed and the message was finally broadcast at noon on the 15th.
This is the most logical explanation, especially given all the other facts you have presented. I am curioius, however. Although the ultimate decision to use the atom bomb on Japan was Truman's, didn't he rely on Stimson for advice, as well as the Manhatten project?