Yes Indigenous land stewardship practices altered the environment and undoubtedly some species were losers and were extirpated. However at a landscape scale, over thousands and thousands of years, the ecology adapted and is most healthy when these practices are applied.

Indigenous peoples see themselves as part of the land not above, so the practices are reciprocal, not exploitative. In this way they achieved sustainability and endured for thousands and thousands of years, whereas colonizers trying to force practices used in Europe have destroyed the ecology in a few hundred years.

Calling Indigenous lands wilderness is incorrect, lands were managed. It's just harder to justify stealing land when you admit that. Same as calling Indigenous peoples hunter gathers when they had sophisticated agricultural practices.