For clarification: are you asking about the ownership of the land through the treaties, or are you asking about the purpose of the unceded land? The latter is easy enough - it's land set aside for hunting and cultivation.

My own area of research is in the Old Northwest and in the Great Lakes region until 1855, but I can answer some generalities for you.

One of the problems with treaties in the years before the War of 1812 and US continental hegemony was that Native groups were not legally defined. This was not a problem for Native groups, as for many, membership of a group was not rigidly defined. To the US, it looked like chaos, and for a while, individual speculators and investors would snap up any bits of Indian land they could, which was difficult for the US government to handle; if individual speculators could purchase Indian territory whenever they pleased, using any number of legalistic means to do it, which complicated the government's ability to gradually expand westward in a controlled manner.

Court cases, naturally, attempted to settle these disputes. Probably the most prominent was Johnson V. M'Intosh (the wiki page linked here, as it gives a decent broad summary) which established that individuals could not legally purchase Indian land.

The reasons that were given hinged on The Discovery Doctrine - the idea that Indians live in a "state of nature" and as such have no legal (because legality is a mark of civilization) claim to the land. They do, however, have "aboriginal title" which essentially states that, by the laws and customs of the United States, indigenous peoples have a use-based claim to the land - i.e. they're on it, they own it.

The tricky thing is that the Discovery Doctrine and aboriginal title are based very favorably on US customs as regard land ownership. Aboriginal title was much easier to claim than title owned by a white man through contract and precedent. Collectively, they mean that Native Americans actually don't own land; they are squatters on land already owned by the federal government.

It gets better!

In order to facilitate the kinds of legal necessities that would constitute a transfer of ownership, the federal government had to define, in explicit terms, what constituted a tribe or native nation. So, essentially, they made them up. Here in Michigan, the federal government defined "The Ottawa Nation" and "The Chippawa Nation" and others in a manner that would have been practically unrecognizable to the groups in question. But, to the US government, it constituted a formal legal arrangement of power, and made land transfer easier and more formalized.

So the problem becomes, if we follow the Discovery Doctrine and the legal precedent of aboriginal claim, what exactly does "unceded territory" mean? In a certain way of looking at it, backed by all the legal inertia in the United States, unceded territory belongs to the federal government.

On the other hand, if it was never ceded, the government has to at least acknowledge ownership (through payment or other compensation) for use or title to the land. If that hasn't been done, do the local Natives own the land? What happens if the government decides to use the land, but the local Natives reject the payment? (which, by the way, has happened at Standing Rock)

That is a lot of what the Standing Rock dispute is about; who is the owner of the land, and who has the rights to use it, if no agreement has been made?

There's really no clear, non-controversial answer. The Natives at Standing Rock are attempting to call attention to the fact that most treaties with the US have been willfully violated, and that the legal precedents established by the United States are deliberately coercive, deceptive, and non-binding (that's stating the case in an extreme way, but how else to describe two hundred years of fraudulence?). The pipeline companies and investors are saying that the legal agreement with the federal government supercedes any land claim made by the Standing Rock tribe.

The answer to your original question is, unfortunately, an elaborate¯_(ツ)_/¯. Native law is extremely complicated, and much of it rests on court cases that set precedent in the 1820s or 30s, and things have not gotten simpler since then. The Standing Rock protest is just the most visible of a huge number of similar disagreements happening all around the country. Land rights, water rights, fishing and hunting rights, basically anything left stated in a treaty that were then discouraged by white settlers and local governments, are now being asserted across the country.

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However, if you'd like to do more reading on the subject, I recommend:

Indian Treaties, 1778-1883, edited by Charles Joseph Kappler. It is a comprehensive list of every treaty signed by the United States with an Indian Nation, with a foreword that restates much of what was said here.

A Spirited Resistance: The North American Indian Struggle for Unity, 1745-1815. by Gregory Dowd. Earlier and more Eastern than you're looking for, but it's a good background for many modern Indian issues.

Custer Died for your Sins: An Indian Manifesto by Vine Deloria jr. A wonderful book that gives an voice to the modern and historical issues faced by Native Americans. It is unapologetically written from the point of view of Natives, and is sometimes off-putting for people who are unprepared for the confrontational tone. But I cannot recommend it enough.

Unfortunately, my research has been around the War of 1812, so a lot of my sources are in that area. Kappler is a great place to start looking, though, and I would of course be willing to offer more of my Great Lakes sources if you're at all interested in those.