Is the red and the green self-contradiction?

[v0031]

Target committee members believed an atom bomb could destroy the infrastructure of Japan without the need for an invasion, so the cities of Kyoto, Hiroshima, Yokohama, Kokura, Niigata, and even Tokyo were identified as potential areas for destruction.

The main criteria included cities not previously bombed by conventional means so that experts could fully assess the effects of a nuclear strike.

Although Tokyo still remained a possibility, it had already suffered extensive damage from a firebombing campaign that incinerated 16 square miles and as many as 100,000 people. In addition, officials believed Emporer Hirohito might still be needed to help negotiate any surrender.

[muon2]

It could be seen as self-contradiction, but there is some nuance in the phrasing that shows how it might not be. It starts with the use of "and even Tokyo" rather than "and Tokyo." This sets up the reader for the possibility that Tokyo is a special case. The second sentence starts with "The main criteria," indicating that there are other unmentioned criteria as well. Finally in third sentence the special nature of Tokyo is revealed. There is even a hint in the final sentence that some target committee members may have thought it desirable to eliminate the Emperor, but were outweighed by those who wanted him alive.

I'm not saying that this is the best written piece. It's not, precisely because of the confusion you may have. I think it would have been better to rearrange it to show that Tokyo was eliminated from consideration for two reasons: it had already been bombed and officials wanted the Emperor alive. However, my way might be more wordy and the writer instead chose to avoid additional text at the expense of clarity.

[angus]

Not necessarily, if one considers the intent of the author.  The point is that the military scientists and engineers wanted to know what was the specific effect of the atomic weapon (and discount spiders, earthquakes, curses, and other sources.)  Tokyo was considered a target, because it is a really good target:  It's huge, it's full of japanese politicians, and its destruction smells strongly of vendetta.  Still, as a scientific experiment it may be contaminated by the effects of conventional bombing, and that was the point of the text that you posted in green.

In other words, the green text doesn't so much contradict as attempt to explain the undesirability of Tokyo as a sterile environment.