"Japanese people make up 98.1%, Chinese 0.5%, Korean 0.4%, and other 1% (includes Filipino, Vietnamese, and Brazilian) of people living in Japan, according to the CIA World Handbook" [1]
So Japan is exactly as ethnically homogenous as you would think.
I've got family in Japan. All you need to do is to go to Japan to see that it's very "japanese".
You can get residency semi-easily but getting citizenship is extremely hard.
It's not the EU or the US where a huge lot of "foreigners" can become citizen.
As far as I can tell from the description of the procedures involved, it's actually easy - and certainly easier than the US, and it requires less time in the country to apply than some European countries. One reason why it's uncommon however could be because Japan does not allow dual citizenship, and it's harder to get into the country in the first place other than teaching English.
You've conflated "citizenship" with "ethnicity".
How enormous? We wouldn’t need words like that if we looked at the right numbers.
> As of 2015, a total of almost 581,000 people have become legally Japanese since the fall of the shogunate and the rise of constitutional "westernized" Japan.
This seems consistent with other sources I found while doing a quick search.
This suggests less than 1% of the number of citizens of japan was not born a citizen.
Of course, some of those people will have children and those children's ethnicity could be not Japanese ethnically (or partially) but still the number of citizens of Japan that are not ethnically Japanese is quite small, and the number of citizens of Japan that are not ethnically east asian is much smaller still.