If you have direct knowledge of how Japanese official process works in practice, could you relate it along with this observation? Because a thing not in much doubt on HN is that Patrick does have some significant experience with it.
Assuming someone at immigration would take the time to look into his background (not just his paperwork), find out that he wrote a Covid-19 white paper with higher projections than the government at the time and then blacklist him for it is such a mischaracterization of Japanese process, I don't know where to start. It's not like there's a source I can reference, but I also have a lot of knowledge of Japanese immigration through knowing plenty of foreigners on different visas in Japan and have never heard of anyone getting rejected if they meet the conditions.
I can share one interesting anecdotal counter-example to show how easygoing Japanese immigration is. Someone I knew was on a fraudulent work visa "working" for a friend. He was actually creating a startup. By the time immigration found out, he had the necessary scale to sponsor his own work visa, so he wrote an apology letter and then switched to his own work visa even though the foundation of the company was built on a fraudulent visa.
I don't know anything in particular about his concerns about his own status. I have, on the other hand, known many LPRs in the US who were extraordinarily careful about their engagement in public matters out of concern about their status.
If your argument is that protection for PRs in Japan is stronger than that of US LPRs, I'm going to go ahead and call that an extraordinary claim. At some point, though, probably rapidly approaching, litigating this point becomes ghoulish. I haven't heard Patrick say he's specifically concerned about his own status, but he's clearly concerned about some of the people he worked with.
That has to be a function of knowing a particular variety of (however reasonably) paranoid LPR's, though, no? I can't imagine it being a core concern for the vast majority of LPRs.