[Rodger Knox]

Now it's golden strings on eagles wings
to the calling of the squares
Now there's fiddle tunes, and there's fiddle tunes
But Virginia's splitting hairs!

Nut compensation is about .012" or so, assume .015". That introduces an error of 0.03" to the measurement. Are you measuring with an instrument that will give that kind of precision over that length? Can you judge the break points at the nut and saddle that accurately?

Average pitch perception is about 3 cents, so for most practical purposes, that's close enough. There are those individuals that can perceive 1 cent, but then nothing sounds in tune to them anyway. That's the nature of equal temperament. There are procedures to get every note on the fretboard within a couple of cents of equal temperament, but that's only beneficial to the most discerning listener. Normal practice of setting intonation at the twelfth fret by adjusting the saddle is almost always good enough, particularly if a little nut compensation is included.