I agree with Al.
I've tried intonating solely using tuners, but i never get entirely satisfied with the results, for some reason.
Jun, on the other hand, is very keen on measurements, just as much as the actual intonation (tuning) of the frets. I guess thats the value added from a bona fide luthier.
one of the first things he does is check kung "tama yung sukat" ng gitara mo. i.e. the fret spacing, the bridge, and the nut. kung may issues about the measurements, iaadjust nya yung nut mo, if it can't be compensated by the bridge.
i can also attest that he doesn't solely rely on measurements and tuners to intonate. he "sweetens" his tuning para maganda resonance ng mga nota, esp. when playing chords sa upper registers. benchmark lang nya yung tuner. pag saliwa sa tenga yung result, Jun will tweak it further.
It's hard to explain, but it's not magic. Neither is it always perfect. but all i know is that it works for me.
Plus he's a straight-up nice guy to deal with, who makes an effort to get to know you and your likes and dislikes. so when you hand him a guitar to work on, he will know what you want from it. so i guess that adds to the experience.