I really appreciate this post. It's hard to read, but this seems very intentional. There are a number of salient points that are very specifically not stated. Some questions deliberately not answered:

Who was on the Working Group, other than Patrick? Dr. Tyler Cowen spread the results, but no one is mentioned as working in the group other than Patrick. This seems designed to limit potential social fallout to other parties. The whole "Someone read between the lines" section would be much easier to read with the relevant person named. Also consider that Patrick may be limiting fallout to himself here, with the bold statement early on that "I instigated the Working Group and I was the primary author of its white paper."

Did the NYT article writer correspond with the Working Group? The white paper was published with plenty of time before the article was written, and the explicit goal of the Working Group was to "leverage a news organization." Also consider that the NYT article was published on Thursday. And when discussing the goals of the working group, "This implied a publication deadline of Thursday. We assumed media organizations would need our work by Wednesday to check it and produce reporting informed by it." Note that Dr. Cowen's quick post was also published on Thursday, possibly to increase deniability when referring to that goal date.

What Japanese organizations failed to respond to this crisis? The most damning prose in the entire article is "May all judgments be just and merciful." Patrick does not identify any Japanese organization or government by name, but says that the Working Group spoke to many of them. Also, both memos are listed in the timeline immediately before a announcement by Governor Koike. Patrick even convolutes his prose to the point where he never mentions the Olympics. I wouldn't be surprised if he had another sporting event in mind that also matched the specifics of what he wrote.

How much influence did the Working Group have in Japan's response? The NYT article is definitely one potential point of influence, but it seems that the memo itself was shared widely. Consider the difference between this humble ending to the article: "I am a responsible professional. I have no relevant expertise or authority. I have avoided unproductive criticism. I might have made some guesses, during a year when many people were guessing on many topics. I quietly told some people about them. Some guesses may, perhaps by happenstance, align with official guidance and credible published reporting." and his tweet confirming the memo (option 1): "I am materially wrong about the most consequential thing I've had to have a view on in 15 years. You should probably degrade your estimate of my ability to think through complex problems."

Interpreting things through an aggressive lens, I read this as a scathing diatribe against the Japanese government, where a non-expert foreigner living in Japan has to get the Western media involved before the government would admit to there being a problem. Props to the governor of Tokyo for being more on top of this than anyone else (perhaps with the Working Group's involvement), but the national government completely dragged its feet until it was forced by international pressure to start asking real questions.

But I'm probably reading too much into it. Patrick's too humble of a guy to say all of that.