I read about how the meat of indigenous people was sold in Qing-era markets in Taiwan, and how the settlers even believed that the body parts of indigenous people had medicinal properties. But I've never heard of cannibalism practiced on "mainland" China, except as a tragic and desperate survival strategy during severe famines. The government officials and other literate-class members who wrote about the practice seem fairly horrified or at least disapproving, so do we know what brought the settlers to do this? Did they view the indigenous people as less than human somehow? And did Han settlers in southwestern China also treat the indigenous populations there in the same way?
Where exactly did you encounter this? To my knowledge, Han Chinese cannibalism is reported in only three primary sources, all written by British authors, and all published after the Japanese annexation of the island in 1895. If you give a specific citation, that would allow some investigation of the claims in question.