Do you know numbers about how much housing is sponsored by the companies in Japan? Maybe that's what is making the difference since it's not counted neither as salary, nor as the price of the house? I know some large companies sponsor partially or totally the housing of thousands of their employees, again skewing prices greatly.
For example if Tanaka's salary is $500 lower because the company is partially paying for their place, that means on paper his salary is lower, the price of the place is MUCH lower, and the ratio of housing/salary is also lower, than if he received those $500 and then used it to pay for the house.