Upvote:3
Mark Savage actually addresses this question in his article, Native Americans and The Constitution published by the American Indian Law Review in 1991. He writes towards the end of this essay that:
Publius discussed Native Americans in four essays. The third essay argued that war powers should be national. A national power would tend to prevent wars with Native Americans which individual states provoked or invited.
Essay 24 argued that standing armies in a time of peace were necessary for protecting the Western Frontier from attacks by Native Americans. Alexander Hamilton added that garrisons on the frontier "will be keys to trade with the Indian nations" and that a standing army was necessary to protect the garrisons from seizure by the British or Spanish.
Essay 25 discussing why this power should be invested in the national government rather than the states, argued that: The territories of Britain, Spain, and the Indian Nations in our neighbourhood, do not border on particular states. But encircle the Union from MAINE to GEORGIA. The danger, though in different degrees, is therefore common. And the means of guarding against it ought in like manner to be the objects of common council and of a common treasury.
Essay 42 discussed two classes of powers vested in the national government, a class of powers "which provide for the harmony and proper intercourse among the States." The power to regulate commerce with foreign nations fell among the former class. The power to regulate commerce among the states and with the Native Americans fell among the latter and was more particularly a species of "restraint imposed on the authority of states."
He also adds:
Insofar as The Federalist is competent evidence of the original understanding, these four essays do not elucidate the meaning of the text [ie the Constitution] but they help to illuminate the intent of the Framers.
In general, Savage argues that the Constitution formally gave the federal government very circumscribed powers over the Native Americans, mostly to do with trade rather than any substantative political or juridicial jurisdiction.