There are, quite literally, third and fourth-generation Korean-Japanese people who are still not considered fully Japanese.

The most famous example is probably: https://en.wikipedia.org/wiki/Yoshihiro_Akiyama

This guy is a fourth-generation Korean-Japanese athlete, but was still never considered Japanese by the Japanese fanbase, he was frequently booed and heckled, and he went on to compete under the S.Korean flag. And this guy's father and grandfather were born in Japan, and he looks ethnically indistinguishable from the Japanese.

It's pure fantasy that second-generation Indonesians or Filipinos are going to integrate into Japanese society. It's going to be extremely painful, if it's attempted.