The ainu and ryukyuan are a tiny fraction of the population

When you count mixed-race Japanese residents as Yamato by default, sure. When you deliberately blot out the historical genealogies as part of the fascist project of the post-Meiji Era, absolutely.

There arent many countries with a lower diversity of population than that.

In the same way that somewhere north of 30% of the population in Vietnam has the last name Nguyen, we can pretend at homogeneity to salve the prickly attitudes people who desire the appearance of a uniform population. Ralphiel Cruz changes his name to Ted. Robert Francis O'Rourke changes his name to Beto. It has nothing to do with their racial composition and everything to do with their efforts to appear to fit in.

But if you believe Japan's 189M people all came out of the same petri dish, you're simply buying into a eugenics myth.