Except they kill humans all the time.
I think it’s just easier to accept that there is an unexplained reason why humans can generate some kind of power that’s useful to the machines for something at some point between the winning of the war at the point of the movies.
Just ignore the fourth movie.
Stark made the suit with no help. He doesn’t need a specific suit because he has the skill to invent whatever he may need.
At this point, Peter can’t make himself a suit like that, so if he is nothing without it, he can’t respect the power it brings. But he isn’t nothing without it, which is what Stark is trying to teach him: not to rely on power of others.