Fresh medium density foam can expand and contract in shipping and pickups are fairly heavy. A good bump can mess with alignment.
But regardless, it has nothing to do with the actual build quality, even if installed slightly one way or the other. Pickups aren't optical, and there’s nowhere near enough room to make a difference tonally. Again, you'll never get it perfectly aligned.
As for ”fixing” it, you loosen them both a couple turns and push in the direction you want it to go. You don't even have To re-drill.
It just seems like such a weird thing to discount a whole brand that makes hundreds of guitars over.
You can't move it this much to compensate that shift unless they drilled the holes in the lugs around 6-7mm in diameter which I highly doubt, to properly shift it you will have to fill the original holes and re-drill them.
It has to do with a poor QC, I can expect that on some cheapo indo guitar, not on a $3k+ semicustom, and I've seen worse from them on even more expensive regiuses where even the pickup routes or bridge was shifted to the side. If you think these things are ok for a high end gear then seems like I can't do anything here