Interesting article. The graphic and the study itself are better than the explanation in the article, which is a bit confusing.
My take: the original Japanese were known as the Jomon people. The previous thesis was that Northeastern Siberians immigrated to Japan during the Yayoi period [3,000 BC - 300 AD], then East Asians (such as Han Chinese) during the Kofun period [starting 300 AD]. The discovery is that a Yayoi period skeleton already possessed all three lineages, suggesting that the mixing of North Siberian and East Asian occurred first, then those mixed people immigrated to Japan. The people who have the closest mix of North Siberian and East Asian are the Koreans, and so the researchers conclude that there was just one migration from Korea that mixed with the indigenous Jomon to create the modern Japanese.
The Japanese have something like a glass floor under which no dated human activity is allowed. It’s dying out. What used to happen was, an archaeologist would dig down until the oldest known/accepted strata was reached, and dig no further. That started to look more and more goofy as time went by, but when a site was obviously deeper (for example, as in other places in the world, a mound) some brave souls decided to dig and found earlier human strata. The professional backlash was hard on the researchers. As in China, the human population of what is now Japan is 100s of 1000s of years old. The barrier is psychological rather than geographical.
Your take is very interesting. My family is from eastern Japan. My daughter had her DNA done and we found we have a lot of Korean in ùs, those from around Hiroshima. That explains why when I was in Afghanistan the locals kept asking if I was Korean.