No big deal, but your installer installed the bolts upside down according to manufacturer's recommendation (instructions). I cannot tell in the photo, as your pre-load spacer looks identical to mine, but I wonder if the spacer was also installed upside down (with the chamfer facing up) which resulted in the extra, unwanted lift.
My RC 1318 kit leveled my truck perfectly, within 1/16". No biggie, angles still look good, and you got alignment. Congratulations on your extra lift haha.