Carefully read the comment to realize this "feel good" piece is written for a western audience: > "This article was clearly written more from ignorance than knowledge and is not based on knowledge of the actual culture in Japan."
The point is that, if you look at official stats and see "98% Japanese", that ignores the fact that many of those people aren't ethnically Japanese, because the stats talk about citizenship, not ethnicity.
I think that comment actually proves the author's point, that there are many categories outside ethnically Japanese, and people there disagree on what it means to "be Japanese", lending credence to the idea that Japan is not a homogeneous society.