Most of the data below came from the following papers:
- 台灣行政區域人口密度: 1640–2008
- 荷蘭時代的臺灣番社戶口表
- 臺灣史上的人口問題
Dutch census, which were limited to a portion of Southern and Northern Taiwan, showed that there were 40 to 60 thousand Plains Aborigines living under Dutch ruled areas. Japanese study showed that based on the Dutch census, total Plains Aboriginal population at the time can be extrapolated to around 350 thousand, and other Aboriginal population at 250 thousand.
Dutch census of Plains Aboriginal villages under their control. Post 1654, the Dutch were losing control of territories in the North and into the mountains, and that’s the reason for a decline in the number of villages and population. As you can see, prior to 1654, Aboriginal population was growing at a rate around 2% annually.
Fast forward to when the Japanese first started conducted census around the 1905, which encompassed a much larger area than the Dutch, they also showed there were still just 40 to 60 thousand Plains Aborigines living in the Western plains.
In terms of population, we should have seen an increase of Pingpu Aborigines across 258 years, especially when the census was conducted over a larger area.
The Dutch introduced some Chinese labor to Taiwan, which by the time they left numbered at 27.5 thousand.
Koxinga and his son brought about 37 thousand troops and officials to Taiwan, and Koxinga occupied a rather small portion of Taiwan as well. There were additional immigrants who followed Koxinga to Taiwan and the number is harder to estimate, but the total Chinese population on the island at the time was no more than 120 thousand. At the same time, Koxinga razed several Aboriginal tribal kingdoms to the ground, massacring entire villages. So we would probably see a decline in Aboriginal population.
When the Qing conquered Koxinga’s Dongning Kingdom, they sent at least 40% of the total Han population back to China.
There are 3 different Taiwan population numbers you could extrapolate from Qing dynasty data.
- The official number, which is people that actually pay taxes. The unit is Rending (人丁) and prior to 1741, that number doesn’t necessary represent male head count in an household. It merely represents the amount of taxes one family needs to pay. An estimate is for every 人丁, there were 4.99 actual people.
- Starting from 1741 (6th year of Qianlong) there is a census based on the Baojia system. This time everyone, including men women and children were counted, as long as they are in the Baojia system. In Taiwan that means if you are an Aborigine, you are not counted.
- The third number can be estimated from the amount of salt sold.
In 1685, when Qing first counted, Rending decreased from 21,320 in the Koxinga era to 12,724, confirming that 40% of Taiwanese Han people were sent back to China. Using the 4.99 times estimate, there were around 63 thousand Han Chinese in Taiwan at the beginning of Qing rule.
By 1688, in a document hilariously called Changing Dynamics of Chinese and Barbarians (華夷變態), which for most people today would mean Hentai Chinese and Barbarians, it mentioned
以前台灣人口甚為繁盛，漢人民兵有數萬人，自隸清以後，居民年年返回泉州、漳州、廈門等地，現僅有數千漢人居住。
Taiwan used to be a very populous place, with Han civilian soldiers numbering to the 10 thousands. Ever since Qing rule, inhabitants were sent back to Quanzhou, Zhangzhou and Xiamen annually. Now there are merely a couple thousand Han Chinese living here.
Which at the time was a pretty small portion of Taiwan, and Qing eventually slowly pushed out to most of the plains, but by the end of the Qing era, they still ruled less than 50% of Taiwan in terms of total area.
Even in 1862, official Chinese map of Fujian province is missing significant portions, and Qing didn’t have control of plenty of regions depicted either. The same goes for Japanese numbers prior to 1919. There were large swath of Aobriginal lands that the Japanese could not freely survey or conduct a census.
In terms of population, there’s not a huge amount of Chinese immigrants flooding Taiwan as you might have imagined. That is because for the most part Qing actively discouraged immigration to Taiwan. By 1737, they even decreed that there can be no further Han Chinese and Aborigine intermarriages, those who broke this rule will be sent back to China.
So between 1691 to 1711 Rending increased by just 755. By the 1711 census, there were 540 thousand Pingpu Aboriginals an estimated 350 thousand other Aboriginals, and just 49 thousand Han Chinese. Han Chinese made up just 5% of the total population.
The population of Taiwan held pretty steady for most of the 1800s. It is only when Japanese civil engineering transformed the productivity of the land that we saw the first population boom.
So if not for mass sinicization of the Plains Aboriginals, what would explain the ratio drastically change between 1711 and 1905, if the population stayed pretty much the same?
The pace of Sinicization didn’t slow during the Japanese era, especially after the Japanese stopped counting Plains Aboriginals separately from other Han Taiwanese, which eventually led us to where we are now.
That’s how illiterate people spell… Similar to the idea of spelling “though” as “tho” 
