The key difference you seem to be missing is, in very simple terms, that organised crime in the West is universally accepted as a negative thing and the people who perpetrate it need to keep their identities and operations secret.
While in Japan, that's not the case: Every Japanese knows what local businesses are run by the Yakuza, knows where local Yakuza headquarter is (it's not hard to find even for foreigners - it's usually a house with 24/7 shuttered windows, high spiked fences, and grim looking guys hanging out in front.
In Italy, that house would get raided in an instant. In Japan, it's just part of the neighborhood, people don't go near it, but otherwise ignore it.
Japan's problems are very unique and no Western country has them. I stand by that. And of course if they want to keep it that way, so be it - but then Japan should not at the same time pretend they're a country of law worthy of a G7 membership. They probably should go back to Sakoku because this two-faced way to be is honourless - and they allegedly put great importance on the concept of "honour", right?
And yes, this is all my personal observation from living in Japan for a couple of years.