Overall, I expect you're right there, Janos. I was thinking more about the sort of official attitude that denies the existence of ethnic minorities, which can in certain cases force the pace of assimilation. I got the impression that that was the process KJI was moaning about in the piece OP quoted. Popular racism would tend to act against that, of course. And I suppose the two effects can coexist - ethnic (or religious) hostility can cause some individuals to seek to assimilate and others to stick together. There are plenty of examples of this in European history; whether the same thing holds true in Japan, I don't know.
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