In the single player story, you’re dragged into an Indian war. Your camp sides with the Natives against the US military out of opportunistic and spiteful reasons, and the elders don’t necessarily approve of it either. But you end up sympathizing with them anyway. It doesn’t try to be “both sides bad,” more like “selfish white men pretending to care about our cause revealed that the US government never had any intentions of being peaceful and fair, and believing they did resulted in more massacres.”

There’s also an arc where you kill slavers and domestic collaborators in imperial not-Cuba (because Cuba also exists in the universe, but the island is based on Cuba and other banana republics). From the dialogue of the guards, it’s implied that the slave rebels are socialists. There’s also a nexus between the corporate slavery in not-Cuba and the American oil companies that employ Pinkertons.

Like could I persistently help grow a native controlled region on the game map or something?

No. Online is just about accumulating and consuming product. The fashion is nice.

Interesting that you ask that. My spouse plays as a native woman and even has a backstory based on real life. As far as I know, there is no native “faction” you can control or anything like that.

To be honest, beyond your appearance there isn’t any difference between player “races” in the game code. So no NPC is ever going to care if you are black, white, native, etc. They probably did that on purpose.

Within the story of the game there are indigenous people, and you can decide whether and how to help them resist the US army. I thought it was respectful although it seemed pretty pessimistic about their predicament at that time. There's a debate between indigenous characters as to what effectively preserving their people means against an enemy like the US.

But I'm a so what do I know.