First of all I'd flag it up with an email to Adam. If it's wrong on yours then it's likely that it's going to be wrong on all the other kits so he needs to get the factory to correct this.

One possible solution is to file the side of the nut back by 1mm. However this will make the nut rather thin and liable to break in the future. You could replace it with something like brass and file that back without the same risks, but it's still a bit of a compromise.

Doing some calcs, the difference in the note frequencies on the first fret will be minimal - about 2.2 cents. You might just detect it by ear, and you'd need more than a basic electronic tuner to do so (which are generally accurate to ±3 cents) - but as I've said, differing fretting pressures can probably make as much or more difference to the pitch as the slight position offset will.

I'd see what Adam says. The factory might need to look into it and change the settings on their neck fretting cutter/router and ship out some replacement necks. However they may have made a conscious decision to move the frets slightly (though it doesn't seem to be that consistent) in order to extend the 1st fretted length slightly to make up for the fact that fretting on the first fret often tends to be a bit sharp if the nut slots are on the high side. But if you've lowered them from the standard factory cut (which is always on the high side) to the bare minimum gap without buzzing, then this effect is very much the same as for all the frets.