Deportation of people who wish to stay and become citizens is wrong. If one has no intention of becoming a part of the new nation, then they don't have to force themselves to stay.
Apply that to what happened in recent history, many Wansei, Taiwan-born Japanese, wished to stay in Taiwan post WW2, and they didn't just want to stay to remain being Japanese nationals, they were staying to be Taiwanese and Chinese nationals since the KMT takeover. Many stated so and begged the KMT to let them stay, but the KMT mass-deported them anyway. That was wrong. So was the deportation of ethnic Germans who wished to stay in various European nations post WW2.
When I say Taiwanese citizens need to self-identify themselves as Taiwanese, I mean they need to want to be Taiwanese citizens. I'm not saying Late Immigrants should self-identify themselves as Holo, Hakka or Aboriginals. So I fail to see how what I've said contradicts with my original statement. You are still mixing the usage of Taiwanese as an ethnicity and Taiwanese as a nationality.
If a person can't even take on identifying themselves as Taiwanese in a national sense, why bother becoming a Taiwanese citizen?