Intonate by fretting.
A pinch harmonic will always be in exact tune with the string you are pinching. If you have a string tuned properly, the 12th fret harmonic will always be an octave higher and perfect. Because: physics.
If your intonation is off, the pinch point (node) may not appear exactly over the 12th fret. The problem is you can't tell by looking. Since the string is not in contact with the fret and your finger is in the way and much wider than the fret, you won't know if the pinch point is ahead or behind the fret. Add in the situation where you can get a sloppy pinch slightly ahead or behind the node and still get a harmonic of sorts to ring and the error in positioning is compounded
If your 12th fret harmonic appears halfway to the 11th or 13th fret, that might tell you something. But the coarse adjustment you make will not be good enough to say that your guitar is properly intonated.
Thus, pinch harmonics tell you next to nothing about intonation are useless for setting it.
However, if you tune your string to pitch and then fret and play at the 12th fret, you will see if the resulting note is too sharp or flat and can therefore adjust the intonation.
One more thing... find a different 'luthier'.