That entire line of reasoning is reliant on truthful answers to a survey that, at least based on my level of Japanese cultural knowledge, would be answered falsely by a significant number because either they mentally argue that not being Japanese is from a different culture not a race, or they have internalised the logic of "we all do this but must not openly say so, because saying so is wrong, but everyone knows we do this anyway, so its ok as long as we don't say this is how we feel". That's just the start of "broad survey interpretation failure" I see here.
You don't think they took those factors into account? They did. Did you even read the article? They didn't ask people outright "Are you a racist?" They tricked people by asking them other indirect questions. Like, "Would you mind if <insert race/nationality> lived next door to you?" Those kinds of questions get to heart of the matter. And they didn't just ask Japan those questions, they asked every country on Earth the same questions.
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.
