Take a look yourself. They did several scientific studies. They found Japan is less racist than France, and equal to most European countries:
Source: https://www.washingtonpost.com/news/worldviews/wp/2013/05/15...
The question just forces the person being asked to think, "Would I mind if this researcher saw me as someone who would mind if a foreigner lived next door to me?" And the degree to which this second-order question matters depends heavily on social mores.
Japan is a country where people are expected from a young age to compartmentalize their tatemae (external appearance) from honne (true thoughts), and consider it perfectly normal to do so. So I wouldn't be surprised if they were simply better at hiding perceived-as-negative sentiments from naive researchers.
Koreans, on the other hand, admire Americans and Western Europeans but look down upon Africans and South/Southeast Asians, and often express outright contempt for the Japanese and Chinese. Depending on their political views, they may even feel socially compelled to express a hatred of one or another nationality. Meanwhile, Korean culture doesn't acknowledge the tatemae/honne distinction, which makes it a lot more difficult for people to compartmentalize.
tl;dr: We're all racists, but some forms of racism are easier to measure.
Not sure if this is one of those things that'll disappear as the newer generations displace the older. Or if the black car squad will somehow keep the attitude alive.
Quite interesting is that there are degrees of zainichi, those who adopt Japanese names and who have assimilated and on the other end those want to retain more of their Korean identity and nationality.
There's also the intersection where some people of Korean ancestry in Japan express sympathies for North Korea, a country which is typically Japan's current arch-enemy,