President Lincoln and the Homestead Act

[Amy L.]

But Lincoln’s conception of “everyone” did not include everyone: The Homestead Act rested on the expropriation of Native American lands.

I am not generally well-read, and I didn't read the whole NYT article, but is that not just what the Homestead Act did?
Is the sentence above not true?

1. The article is about how the US can improve today, so certainly the shadow is cast in today's contemporary light. What are next best steps? What mistakes were made in the past?

2. It seems appropriate that the New York Times qualifies the benefits of the Homestead Act, and at least partially rests (as figurehead for the State) responsibility for the 1863 bill on Lincoln. Lincoln also proudly wrote of it in his Annual Messages.

For one thing, the Office of Indian Affairs was the most corrupt department in the US gov’t, and Lincoln knew this. He said:
“Bishop, a man thought that monkeys could pick cotton better than negroes could because they were quicker and their fingers were smaller. He turned a lot of them into his cotton field, but he found that it took two overseers to watch one monkey. It needs more than one honest man to watch one Indian Agent.”
Although knowing this, Lincoln could have started reforming the broken system, but he simply directed Caleb Smith, “Please make out… blank appointments for all Indian places to service in Wisconsin [and Minnesota] in favor of the persons united recommended by the [State] Congressional Delegation.”

From Lincoln’s 1863 Annual Message -
"The measures provided at your last session for the removal of certain Indian tribes have been carried into effect. [Treaties] contain stipulations for extinguishing the possessory rights of the Indians to large and valuable tracts of land.”
And what is left for the Indians, whose land the settlers simply take, or cunningly con from them? The European Americans made the rules and the game, all to their insatiable advantage.

Lincoln was of the spirit of Manifest Destiny and we now look at those policies and values as self-serving and immoral. The NYT side-comment covers bases.