On the same ¥11,000,000 gross, a worker takes home roughly ₩1,981,600 more per year in South Korea than in Japan. That gap reflects the tax structure alone — before rent, healthcare, or savings behaviour come into play.
Housing is the first multiplier. South Korea has high rent pressure, while Japan has moderate rent pressure. That means part of the higher take-home in South Korea can be absorbed by rent if you land in a major city.
Healthcare and pensions go in the opposite direction. South Korea runs a universal healthcare model — National Health Insurance covers almost all residents. Japan uses a universal model — Universal Shakai Hoken with 30% patient co-pay; very low absolute costs. The country with lower take-home often shifts costs that the other country leaves to your private budget.
Net-of-everything, a relocation decision should weigh strong public welfare in South Korea against comprehensive welfare state in Japan, plus differences in pension capture, social safety nets, and city-level cost of living.