Philippines is a bad example as before the Spanish and American colonial periods Filipinos were already a distinct ethnic group.
Except for the Aboriginal people, Taiwanese have prior to 1895 been Chinese and subjects of the Ming and Qing Dynasties. I cannot recall any movement prior to the 20th Century that demanded independence for Taiwan or promoted a local, distinctly Taiwanese identity. People lived their lives first as part of Fujian Province and later Taiwan Province - Beijing was far away and nobody really cared about the Taiwanese. Taiwanese have not been deprived of statehood o anything else.
Filipinos however were forced into a colonial regime and did not rule their homeland themselves. Im fact their situation could was more that of Taiwanese Aboriginals than that of the so called "Taiwanese" (=> ethnic Chinese).
Korea on the other hand is a far more fitting comparison.
And regarding your last point: 100% correct! It bothers me that some people claim in 1945 or 1947 or 1949 Taiwanese wanted independence and that there was some kind of independence struggle.
Taiwanese sent elected delegates to the constitutional referendum in 1947 - there must have been quite a few locals who were pro-Chinese integration.
Besides, people should not mistake the democratization that took part inside the KMT and government agencies with the protests on the street by pro-DPP activists. The KMT could have just as well chosen a "Beijing solution" and let tanks roll through Taipei. Yet by itself the KMT chose democracy. It's not like there was anything to win: recognition for the ROC was already gome by the 1970s and as we can see, even free and open presidential elections that took part since the 1990s did not compel any major country to recognize Taiwan.