Hiya Kevin,

the measurement should be from the front of the nut, to the centre of the 12th fret itself, not the 12th fret markers.
As long as you can set the saddles to their mid point of adjustment, replicate that nut to 12th fret distance you should be okay.
If it looks terribly wrong, i.e. bridge interferes with bridge pickup rout, then we'll need to do some further investigation, or you might need to call in Adam and the PBG team.