I've also just recently received my SE DGT MTS and absolutely love it. Feels great in the hands and the pickups are amazing - I've had SE's before and never loved the stock pickups, but these are amazing.
However, I do have a couple of QA gripes about this guitar. The worst was that the nut was not flush with the fretboard on one side - it was about 0.5 mm recessed - very poor of PRS to let it out of the factory with that . Took about 30 mins with sandpaper to fix. The next was that 3/6 screws on the tuner keys and 4/5 screws on the wiring cover-plate were stripped and could not be tightened - very sloppy work from the person drilling these holes and completely unacceptable - it's been reported before by others so if you're reading this PRS please fix it, it's an easy fix. Also some of the frets had scratches and marks on them and needed to be polished. The action was too high but that was easy to fix
Apart from these issues which I managed to fix it is a great guitar and a joy to play.
PS: I'm in Australia and I don't think anyone looks at the guitar once it leaves the Indo factory. I believe in the USA that PRS go over the guitars before dispatch so maybe they pick up these things in that process??