If anything the Jomon (the original inhabitants) were probably "lighter" than the invading Daimyo and Royal Family conquerers in the mid 500s.
In general Japanese skin tones vary tremendously. WITHIN A SINGLE FAMILY ~ particularly if it's a Daimyo family, you will have people as light and pink as a Swede, and those who, given a good day's Sun out at the beach, will literally be as black as a Samoan!
To the degree melanin concentration or the absence thereof is of selective advantage to a human population, the Japanese, in my experience, have the broadest available changes. They can be light, or dark, or in-between. Same with the Sakha/Yakuts ~ and they spent thousands of years running trade routes from Siberia to Nepal!
Some Koreans exhibit the same characteristics ~ but again, their old Ruling Elite was totally suppressed under Japanese occupation and most of them were executed. The Yi family had a good number of escapees, and they tend to be lighter, but more Chinese looking than other Koreans.
Still, given all of that the greatest remaining mystery about the Japanese is why they have such a large admixture of Polynesian words in their language. This is definitely post Ice Age stuff, so where did it come from?
I am digging this thread!