I don't see how the long-term contract is financially worthwhile.
Basic salary 15,336,000JPY + (12 x 50,000JPY commuting allowance) + 2,000,000JPY joining bonus = 17,936,000JPY.
33% income tax + 10% inhabitant tax ~ 7,700,000JPY, leaving you 10,236,000JPY + annual bonus which is profit dependent.
This equates to a net salary of 85,000USD + annual bonus. This also does not take into account the reduced training salary + health and pension which the pilot must contribute 50% and the company the remaining 50℅.
Short-term contract assuming 50% tax on the taxable items and not taking into account reduced training salary equates to 95,000USD per year.
Above figures dont include layover or early sign-on/late start allowance or 6 Y class tickets home, but this would be the same for both contract types.
I suspect the weak JPY is dragging down the USD value, but factor in the cost of living in Japan and the 6 months training even for a type rated pilot - this makes Vietnamese contracts look good!