Some luthiers and set-up experts actually intonate a guitar very slightly flat when doing a “bench” setup. The reasoning is that on the bench, the technician can use the minimum amount of pressure to fret the string, maintaining constant tension and stretch to the string. But when the player takes the instrument onstage, all bets are off, and he or she will likely use a tighter grip, resulting in the guitar playing sharp.
This is also a reason that your tech should watch you play your guitar before intonating it — to get a good idea of how hard you squeeze the strings when playing. The intonation can then be set accordingly.