If you look at almost any kind of cross-national data, you notice that East Asians are fundamentally different from other peoples. So much so that we might talk about an “East Asian package,” a series of traits shared by South Korea, Japan, China, and the Chinese-descended nations and territories of Hong Kong, Macau, Singapore, and Taiwan. There are indications that even North Korea shares many of its important components, despite it being the most isolated country in the world. This package includes:
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The East Asian countries in question all have a history of strong (compared to their central and southeast Asian neighbors) central government. They also have a history of literacy. And they aren't independent: the origins of both the Japanese and Korean legal traditions lie in the Chinese classics.
He only mentions Confucianism in passing, and that seems like the elephant in the room. I've lived in both South Korea and China, and the respect for hierarchy and harmony and emphasis on self-improvement through hard work and education permeate both cultures. Also, elite Koreans used Chinese script to communicate (Korea didn't have its own written language until the Middle Ages), and Japanese readers can understand a lot of written Chinese in ways that English readers can't understand German. Elites in all cultures were heavily influenced by Confucianism and China throughout history, and these trickled down over time to the masses. If it is genetics, we have ample Korean adoptees to study, and nothing has yet turned up.