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.