I really don't know what the point of this article is, it hasn't answer the question it poses. It simply starts with a straw man argument that Japan is only thought of as homogenous because of the 2% foreign-born statistic.
Firstly, that 2% statistic is telling, even though he pretends it isn't. It doesn't tell the whole story, but it is one of the best indicators for homogeneity, because the percentage of people born abroad living in your country, says something about the recent (last 2-3 generations) inflow of foreign elements (e.g. language, food, dna, religion etc).
If you look at the statistics, Europe and the US are places where these percentages are very high. The US or Germany for example are around 15%. Given Japan is at 2%, that's actually 1 out of 50 in Japan vs 1 out of 6 in say US or Germany, a massive difference.
https://en.wikipedia.org/wiki/List_of_sovereign_states_and_d...
Second, even if you look at the population which is born in Japan but has a non-Japanese heritage, the very fact so many blend in and aren't known to have non-Japanese roots says something about the homogeneity as well. The author references Masayoshi Son who is seen to be Japanese and only known to be Korean due to being a billionaire that journalists looked in to, isn't an argument against homogeneity (because, look, Koreans in Japan! Didn't think that did you?) but rather for homogeneity (because look, a 3rd generation Korean like Son isn't normally recognised unless he is a billionaire. Their entire culture has blended in and become Japanese to the point it is homogeneous and only detectable by DNA-test or investigative journalism. That shouts homogeneity to me. Son needed to be famous to be recognised as Korean ,not Japanese. But Obama or Harris didn't need to be famous to be recognised as different from the majority ethnic group in the US.
People don't claim that Japan is completely racially pure. The claim is if you take a homogenous/heterogeneous spectrum and plot rich countries on it (e.g. EU, North-America, Australia etc), Japan is relative to such countries, much more on one side than the other.
There are two main reasons for this. One is that Japan simply has had much less (permanent) migration for one.
And two, even with high-levels of migration, there can still be two different responses: Integration or Assimilation. Star Trek's Borg are fully composed of new peoples, but they are assimilated. Everyone becomes Borg, unrecognisable. Whereas you can also integrate new peoples, your culture changes, you adapt to new elements, the population and the individuals therein can be recognisably differentiated. Japan is no Borg, but on this spectrum it also scores higher on assimilation than integration, vis-a-vis other rich countries like the US or Europe. And in that sense, Japan is among a few uniquely (relatively) homogenous countries.