I think people who clap back like this assume the indigenous groups were able to negotiate with full, symmetrical information and legal leverage. The article reflects history in this regard, suggesting that they did not.
Finally of course there is the "So what" aspect of it, I don't think anyone seriously argues that the US or other strong powers simply mow down the sovereignty of countries because they abuse their own citizens. If you want to advocate for a single world government that is another issue entirely.
[1] https://www.brookings.edu/wp-content/uploads/2016/07/Chinas-...