Patience and precision + good eyes glasses etc, a little trick I sometimes use is that I overtighten the truss rod so the neck is pulling back. If your going for the ultimate low nut cut this can sometimes get you out of trouble if you go one swipe with the nut file too many as when you release the rod it should raise the slot as the neck pulls up. I usually try and cut the nut to the tuning so e sharp should be when fretted on the first fret and so on. Nuts and laquer dings are a complete PITA !!
If we are not good people in life, we will end up fixing lacquer dings on edges in eternity, and drinking the drops quarter fingers of beer left behind in the sun from wasteful drinkers.
I see the nut as an opportunity, though - it pretty much makes the intonation on a guitar and it's fairly easy work if you're willing to cut one low and then fill it to get it dead nuts. I used to try to use a shim, but it's not accurate enough, and then there's always enough time between guitars that I think "I'll bet that could go a bit lower" and buzz on G or B.
Fortunately, i only play about 5-10 hours a year some years, so nothing bothers me that much about guitars.