I assume by “the nationalists” you mean the KMT, but the large migration of the Han to the island happened in the 1600s.

And doing a little more research (thanks for the impetus) it looks like that migration was a process that was initially driven by the Dutch East India Company.

Then it was driven by occupying it with Chinese military to keep the Dutch out.

But that process never stopped and Han settlers became dominant over the next century.

Then the Japanese imperialized. Then the KMT terrorized it.

But the original indigenous people still live there and the national question will likely arise at some point after reintegration.