OP was specifically asking about 2016 when he first got here. He got here nov 2016, and obviously was a non-resident for 2016 (less than 90 days). his question was specifically on why his money was withheld in 2016 (not 2017 or 2018, which like you said, he was a full resident, and as such everything else you said is true). remember, residency is on a per-tax year basis, so it doesn’t go backwards in time to the previous year. jan 1 to dec 31 is all that matters.
but he was specifically asking about why he was withheld and taxed in 2016, because he (incorrectly) thought that by being in taiwan less than 90 days during the 2016 tax year, he should not have been taxed.
i was explaining to him why he thought that. it was because he read about the less than 90 day foreign employer exemption and thought that it applied to all income. and i was saying ‘you probably got confused about that, the less than 90 days tax exemption only applies to income you made from a foreign employer, not money you made in taiwan from a taiwan employer’. everyone else answered about how he owes taxes for 2016 - i wanted to explain why he had that mistaken idea about < 90 days being special (because it is, for foreign employer income).
this 90 day exemption means that someone can work in taiwan for 89 days but not be taxed if their employer and income are foreign (like a US company paying into a us bank account, but sending an employee to taiwan to work for 89 days). it ALSO means though that if i take a sabbatical and just chill in taiwan for 100 days (no working), then taiwan will expect me to file taxes for that tax year, and well at this point they will want a prorated cut of my annual income, or i’ll have to convince them that i wasn’t working, but either way, this will be extremely messy.