Your challenge is to have at least some of Taiwan under the control of its indigenous peoples throughout the vast majority of its history. You can use whatever POD you'd like.
The best candidate would be a sinic or indic polities taking over Formosa, with the Taiwanese as the underclass. This allows reorientation of the society away from tribal affiliation to state-system. Eventually the polity becomes more native with a formosan language becoming the official language.
I shared the same scenario as @Anawrahta , the only difference is that I think it would be applied to both Minyue and Wuyue* as well, who were possibly related to indigenous Taiwanese (they're indeed Austronesians) ; thus, the island would be included in such zone.
*OTL Jiangnan region (southern Jiangsu, Shanghai and Zhejiang) and Fujian.
The indigenous Negrito population of Taiwan unifies and begins to push against native Taiwanese polities, causing different Taiwanese groups to basically become Vikings, as opposed to otl where only one group of Taiwanese aboriginals is the ancestor of all Austronesians.