It's probably not a great analogy but, I think that if you were in e.g. the USA and there was use of White American Judicial System, or White American Police Force or something along those lines it would really scream out at you.
I realise he is out of Japan now and the blog post is not necessarily targeting people in Japan, but a lot of foreigners in Japan will prefix Japanese things, people, institutions etc with the adjective Japanese, particularly when talking about negative experiences or encounters.
When really the adjective should be redundant in those environments.
And yes I agree that the Japanese penal system is terrible. But the problem is more the continual strong association and reinforcement with everything and everyone Japanese.
He could have explained why he chose to leave Japan and then stop the continual references. I'm positing that the continual references, throughout the article, to Japan and Japanese people etc are both overkill and could reflect inherent biases. I'm not saying they definitely do, but I think he'd have an easier time if he stopped associating the negative things in general with Japan and Japanese people and attributed them more to the specific situations, institutions and people.
Within context: "The police are awful" is better for your mental health than "The Japanese police are awful".