I would think you could loosen the U bolts and shift the center pin within the mounting pad as much as possible. Here's how you would know if it's 'factory'.
Measure from a common place on both sides such as the flange where the brake dust plate mounts. Measure from here....to the center of the pad where the leaf spring sits,.....on both sides.
If there is a difference in that measurement, then you know where you're problem lies. If it's the same, then something else is out of whack. If possible, find another x runner in your area and compare measurements. I find it hard to believe Toyota would have that much of a difference on purpose.