I don't know. After Contraband came out, I wrote to Doug Grean on MySpace about all the vocal layering, and he wrote back saying he was just talking about that with another singer and how much he hates it. He said it's easy to layer a bunch of average takes on top of each other. It's hard work to do one great take, and Scott can be lazy.
Within that context, I don't think it's a coincidence that the best Scott has sounded in 10 years was on Libertad. I mean he sounds great the whole record, but Gravedancer and Messages, especially, he sounds as good as he ever has.
I think that is the value of having someone who can constructively push you. I think that's why the band didn't like Rick Rubin for that record. From what I understand, he comes in every so often, listens, tells you what he likes, but on the ones he does like, he tells you the take isn't there yet, and he leaves.
O'Brien is a musician himself, he comes up with song ideas, and I think someone like Scott has an easier time taking criticism from someone of Brendan's stature.
What I am saying is, I don't think this was used purposely as an effect like say, we all first heard it when Cher used it in that believe song. I think it's being used to make sure he is in tune. I think he did a run through that was good enough to perfect with autotune. Problem is, the more off pitch you are, the less human it sounds, which is why we can hear it.
It just doesn't make sense that it is used as an effect, at least to me.
EDIT: On a hunch I went back to some live versions. Live, he plays this in F. The studio version here is in G, a whole note, or two-half steps higher. He isn't that great live in F in the versions I hear. Yet another reason to use auto tune if he is having problems a whole note lower.