Even up to the late 1800's, the Chinese government was unable to control the Taiwanese aborigines. Seriously, Japan won't be able to control Taiwan until the 1800's.
Which is why you'd end up with a somewhat marginal society clustered around centers of Japanese control until the Japanese government could bring the Taiwanese Aboriginals to submission at a later date. No, life wouldn't be pleasant for the majority of Japanese in TTL Taiwan, since most would be living in constant fear of Aboriginal raids, but the island would be important since it's again, right on the doorstep with China. I'm not saying that Taiwan becomes part of the Home Islands of Japan or anything (Sakhalin probably would in this scenario, though), I'm just saying that Japan here would be able to put up a serious fight for the island against both China AND Aboriginal peoples. The Taiwanese Aborigines are definitely a severe issue for Japanese colonisation and they could and probably would play off various powers (Japan, China, possibly European powers) against each other as the situation at the moment called for.