There are so many keyboard layouts for different countries and variations thereof. I very much doubt it's hand-positioned. The layout is not that hard, you can use a fairly straighforward linear constraint solver to lay it out on various different screen sizes. Surely at this level of localization it's more than an afternoon's worth, but I it's not hard in the grand scheme of things.
Maybe it's not quite hand-positioned for every screen, but with the level of detail necessary in the constraints for a constraint solver to be able to do it, I think that might as well be considered hand-positioning in some sense.
Also, it's only anecdotal, but in ~10 years of installing day-1 betas of iOS, I've yet to see an autolayout bug on the keyboard. Admittedly I'm using British English which I'm sure sees a lot of QA testing, but incorrect constraints would probably be a hot spot for issues, and I've seen autolayout bugs in a ton of other software, so my guess is still that it's not really that automated.
