Toyama, the one I searched to poke holes into the argument:

“1.87 square miles (4.8 km2), or about 99.5 percent, of the urban center was destroyed.”

That makes it a 2.2km square destroyed, which for a 150,000-person city is certainly far from a destroyed city.

“Even the most hardline leaders in Japan’s government knew that the war could not go on. The question was not whether to continue, but how to bring the war to a close under the best terms possible.”

This is absolutely not true. They were planning to win or die, and expecting to win.

The battle of Okinawa proved that they could win. America could not, would not, pay that price a second time.

What turned the tide was a false intelligence report that the Americans had thousands of nuclear weapons, and were intending to carpet bomb Japan with them.

1) Those millions of soldiers dug in on the beaches aren’t perpetual motion machines. They have to be fed, if nothing else and Japan in 1945 was a starving nation. As you point out, the US Navy had cut off all external sources of supply to the home islands and it was only a matter of time (months?) before the fighting strength of their soldiers was critically diminished. Remember that we were planning to go in with everything in our arsenal, chemical weapons included, and that they knew that.

2) It’s true that we had smashed many of Japan’s cities with conventional bombing raids, but those raids involved hundreds or even thousands of bombers hitting the target zone in waves over the course of hours. The fact that one B-29 with one bomb was able to smash a city was an unimaginable escalation. Without 20/20 hindsight (which Wilson seems to take unabashed advantage of) how was the Emperor to know we couldn’t destroy every remaining population center in Japan over the next few months, only to then start on agricultural areas and troop concentrations?

3) In all his reasoning, Wilson never mentions the point at which the Japanese leadership suddenly became rational in their conduct of the war. I haven’t been able to find one. Didn’t a group of generals even try to jump the Emperor on his way to broadcast the surrender message?