The article said "the survey question is a way of judging racial tolerance but, like many social science metrics, is indirect and imperfect."
It seems to me that the question illuminates racism among countries regardless of an honest answer. If, to the question "Would you tolerate a neighbor of a different race," a respondent honestly answers Yes, then we can conclude he or she is not racist. If he or she dishonestly answers Yes, then we can conclude that the society stigmatizes open expressions of racism (assuming we're dealing with a rational person).
A yes answer, therefore, gives some indication of racial tolerance in a society irrespective of its honesty.
Is that not a reasonable conclusion?
It probably does say something about a mixture individual prejudices and how the individual believes those prejudices will be perceived. Though I partly think, why not just ask 'Do you judge people on the basis of their race?'.
But I'm not convinced that tells us a great deal. For one thing it perhaps depends on how much contact with other races the person has, which means it could be that the prejudice is inversely related to the chance to actually act on the prejudice. For another I don't think 'racism' is just a matter of conscious prejudices held by individuals. It is also structural and insofar as it is so, individuals don't actually _need_ to be personally racist.
Also there's this international comparison, which seems to use a slightly cleverer metric (a rapid-association test), but seems to have similar results, though I don't know where to find data for countries beyond Europe.
Again, though, racism is also a structural thing, not purely a matter of what is in the heads of individuals.
(Plus, I suspect the really bad results for Czechs is because they are thinking of Romany people, rather than Africans, not that that's an excuse of course, but 'racism' is going to be directed at different groups depending on the context, which does raise the question of 'if there's nobody there to be racist at, is it still racism?')
https://figshare.com/s/730b15bec39c1908cb31