Someone far more knowledgable than I needs to answer this, but weren't most "indian territories" outside of the US at the time of the ratification of the constitution, and thus technically the US developed around them.
Indian territories were merged with US territories to create states. Oklahoma indian territory for one, merged in 1906 or somewhere around there to create the state of Oklahoma.
Oklahoma could not become a state unless while the indian territory remained a separate tribal ‘nation’.
You’ll be interested to know that the UN promotes the idea of sovereign nations for tribes and indigenous groups within the borders of countries, because it creates disunity and dissolves national authority over them. See Kosovo for more information.