There were Chinese fishermen there and perhaps a few other colonists. Even though it still did not become a part of the area we know as China until the Manchurians conquered the remnants of the Ming there.
indeed, lots parts of taiwan was not under effective chinese administration until qing, that is why i use the word colony, not territory.
but it is also wrong to say only a few chinese were on taiwan island before qing conquered it. although officially, chinese govs did not encourage people to migrate to taiwan, civilians were much much more curious to be there. not only fishmen, but also traders/smugglers/pirates, and the basement of them -- farmers. they had significant development during ming, due to wokou intrusion, isolation policy and starving. the most famous one was the last wave leaded by yan si qi and his follower zheng zhi long, the later is the father of the famous koxinga.
so, officially, it was not under effective control of chinese goverments. but was indeed under effective development of chinese
the ones conquered by Qing were not aboriginal people, that is my point
