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.