Thanks for bringing this up, yuanzhumin, it's an often unknown and neglected part of Taiwanese, Japanese, and WW2 history.
You're right, it is a sensitive subject... and I think partly because Taiwanese peoples have always been greatly influenced by their larger neighbors... and finding identity can be hard. Throughout their history, Taiwanese, ben-di-zhun and yuanzhumin, felt somewhat distinct from their neighbors... but the Japanese occupation had profound affects, severely defeating and alienating the peoples, yet in many ways, transforming them into a very productive and loyal society... many Taiwanese were educated/indoctrinated in the Japanese system. For example, my grandfather can speak Taiwanese (hoklo) and Japanese, but much less Mandarin...
It seems despite initial sporadic guerrilla resistance by Han people, the aborigines put up the most defiant resistance (possibly because of the defensive advantage of living in mountains)... and ironically they became some very adept jungle-warfare troops for the Japanese empire... but I also think part of that is Japanese racial and cultural discrimination - they looked down on Taiwanese in general as barbarians, but Han Taiwanese as cowardly and greedy, while they saw Aboriginal Taiwanese as brave savages... almost like European notions of "noble savage" and "martial race"...
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