precisely why I use the 15th fret - there is no donimant harmonic there to distract the tuner
the reason we intonate an instrument is to account for the string stretching that happens when we press down on the string and cause it to contact the fret. since the string is being stretched slightly sharp (more so if you have really high action and/or heavy strings) the saddles are moved back from theoretical scale length location to accommodate this sharpening of the note and bring it back to being in tune. utilizing a harmonic on an open string really does little to impart the stretching quality of playing a note, and using a major harmonic node only gives room for a tuner to catch the harmonic instead of the lower fundimental
my set-up process is to do things in roughly this order (given that the frets are properly leveled)
- tune all strings to pitch
- adjust neck relief
- tune all strings to pitch
- adjust individual string heights for preferred playing action
- address any high frets with 600 grit sandpaper in cases where the action is sickeningly low and the frets have already been leveled. this is where a good set-up guy earns his keep from a player's perspective
- tune all strings to pitch
- intonate each string, making sure that I always tune up to pitch so that the string is under tension on the peghead. the 15th fret is my usual starting point, but I also reference the 17th and 19th frets on basses I know will be played by someone who really gets around up high on the fretboard.
- play a series of notes up/down the neck on each string, various double stops, and then open string + harmonics to ensure that everything is a-OK
on occasion I find an instrument someone's brought in for a set-up that will intonate correctly, but that has a fret or two in the 5th - 9th area that is ever so slightly out when everything else is in. usually it's been because the fret crown in that area is a little off of direct center - but it's never been enough that anyone except a fretless player with ultra extrodinary super-human pitch discernment would catch it in a studio setting