They already shimmed it. My point was that with that scope and mount, it sounds like something wasn't done properly if you have to shim it from the get go because you're already out of adjustment just trying to bore sight it. I feel they either didn't know what they were doing or there is a problem with the mount, or lastly with the scope.
Let me add more about my experiences with adding shims on my AR with the PEPR mount.
Depending on the scope it only has so much adjustment. My photon XT had to be shimmed, works off of a X/Y coordinate. only has 30+ and 30- for elevation. It sits higher on an AR and the scope doesn't have as much adjustment as say a normal 3x9-40. I was also told sometimes the rail on top of the AR isn't perfect and to check a couple different slots to see if it was get better. This would point to the rail on the AR having an issue. I moved mine around and it didn't help. Only thing I didn't do was flip the mount around to see if it corrected it the complete opposite. So if I was 4 inches high, I would be 4 inches low. That would point to the mount. I just added the shim and moved on with my day. Hope that answers some of your question as to why it was needed.
I don't know if it was the top of my AR or the mount. Maybe one of these days I will spend the time figuring it out.