In Lightroom 4.0 (did not check the release candidates 1 or 2 for 4.1) auto-tone (apart from current issues) applies to the full image not post-crop. This is a problem with scanned photos (paper photos, not film) where the borders contribute significantly (and falsely) to the overall analysis for auto-tone. Large white borders (which you would hardly ever keep for a scanned photo) distract auto-tone function.
With the potential of a great auto-tone available in 4.1, I would like to crop the thousand strong photos, then apply auto-tone to fix them up as best it can before manually reviewing/adjusting each one.