OP's point is that this is often overblown. Plenty of ancient civilizations ran themselves into the ground through environmental collapse. I'm currently reading The Big Oyster, which documents evidence of the native population over-harvesting the New York harbor.
Almost by definition, a colonist will be part of a more-powerful civilization than the indigenous populations she encounters. Bigger civilizations have bigger footprints. It takes care to disentangle which cultures are inherently more "at balance" with nature, i.e. could scale less destructively, versus those which are scale limited. (For example, Nordic versus Continental culture, for European examples.)
Using that idea of "legibility" that Scott proposes, not accounting for indigenous "tribal knowledge" in planning for their "betterment" does not work. Common language that reflects this happening is when such knowledge is trivialized or rejected using words like "unscientific".
[1] https://www.amazon.com/Seeing-like-State-Certain-Condition/d...
While I agree with this sentiment, I think it's still really important to recognize the deep ecological knowledge that indigenous peoples have of their environments. The Cahuilla people, who are indigenous to where I live, for example have always had botanical experimentation deeply integrated in their cultures. Some of the most important people in their cultures were botanists. They had many complex rules around patches of certain plants growing and these important people (who I'll just call "doctors" as an insufficient translation) would claim certain patches and study them for years. Some of this knowledge was shared with the rest of the communities, while some was protected and only shared with their close family members or apprentices. Their "folk taxonomy" had names for every single species of oak that is recognized today in the area. An extremely impressive task given how readily many species hybridize
The same can be said of many indigenous peoples around the world. There's an increasing recognition that the Amazon isn't just some pristine wilderness but rather a "manufactured landscape" that has been deeply shaped by the indigenous caretakers of it. In fact there's also an increasing recognition that oftentimes "conservation" ends up hurting the environments it's trying to protect because it kicks out the indigenous people that the landscape relies on. This can also be seen in California where so much of the ecology is dependent on the cultural burn practices of native Californians