Their family probably came to Taiwan after the Japanese invasion. 

Japan was notoriously brutal to the indigenous population, but most of the people in Taiwan came there in the civil war. 

In fact, stamping out the indigenous culture has been an ongoing part of the post civil war Taiwanese government, and it's only recently that the Taiwanese language has been allowed to be taught in schools.

To be fair, the Japanese occupation of Taiwan ended in 1945, so who knows what you're friend is basing that on.