I think the most important point he's making is that these kinds of auteurs still exist, but that they've lost their place in the changing structures of Japanese companies.
The companies previously depending on them realised that they don't need an expert developer with decades of experience, game design knowledge and leadership qualities to put out pachinko/gambling mobile games.
It's an article that was a long time coming. The list of respected (legendary?) game developers that split from their respective home companies is extensive and sobering. Kojima is just the latest.
If anything I see Miyazaki at FROM, The continued existence of Platinum and Tabata at Square as the first legit replacements for a lot of the big name Japanese talent that have sort of been the same for the last 10+ years.
Now you would have to be lying to yourself to think the Japanese industry is anywhere near as healthy as it was a few years ago but it does seem we are finally seeing some new faces to a sector of the industry that seemed like it was dominated by the same faces that popped up during the PS1 era.
This is also an important point, but I think there's still a difference between a generational changing of the guard within a company, and these legendary game designers being ousted/leaving their decade-old home companies.
Something like Splatoon, headed by the next generation of game designers at Nintendo is simply a generational change that has to happen at some point, but the Kojima (and Iga, and Mikami, and Inafune etc) situations would be like Miyamoto or Aonuma suddenly being forced to leave Nintendo.