Not correct!
You're not paid by Air Japan, you're paid by the contracting agency. You are paid gross and it is up to you to sort out your tax. The number of days we stay in Japan does not affect AJX one iota because they have nothing whatsoever to do with our salary or our tax apart from giving the agencies the money to pay us.
We have Japanese with JCAB ATPLs flying for AJX i.e. NOT Mainline ANA. They are hired by the same contracting agencies as non-Japanese. They are also paid gross and expected to take care of their own tax affairs.
What you're saying may apply to other contracts where the company pays the pilots directly. This is NOT the case with AJX, so what you've said is incorrect for this situation.