My truck sits at stock height and one screw is waaaaayyyyyy lower than the other one. It's almost lower than the frame rail. It's been that way forever. I know cuz I got under there once and looked at it myself.
I guess I'm lucky I haven't ever sheared it off on a rock or a curb at the mall
Sorry I can't give you a technical breakdown of WHY it's that way, but that's how it's aligned. If you can reindex them, that's what I'd do, cuz if I were you I'd be really picky.