@Bogner,
thank you for your in depth reply, but still, the nut is OK. I have built and/or replaced the nuts on most of my guitars. On all my guitars the string distance from the edge of the fingerboard is the same on both sides, at the nut and at the last fret.
That is why I am "questioning" this guitar.
The GrapTech 6643 nut does fit my PRS SE perfectly, but not this guitar.
Another thing to note, the guitar came from the factory with a black tusq nut. Maybe because its a lefty guitar.
I agree, the bridge placement can't be off. All the body routing is done with CNC including the bridge/tremolo mounting holes and the bridge pickup ring mounting holes. The neck pickup ring mounting holes are drilled during final assembly, when the strings are already on the guitar...
If the nut is installed correctly, the bridge is positioned correctly, the only remaining point of "failure" is how the neck was installed.
Here is the picture of a straight edge parallel to the neck on the low E side:
drive.google.com
The edge of the neck is parallel to the straight edge all the way.
straight edge parallel to the neck on the high e side:
drive.google.com
The neck tapers off leaving a small gap.