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Intonation question.

The advantage of fretting the 12th fret is that you can hear/compare the exact pitch of the 12th fretted note against the 12th fret harmonic. For example, when you fret a note you are stretching the string, I know its only about 0.2mm or less but its enough bring the pitch up, sharpen it slightly that is.
Since you'll always be stretching the string everytime you fret a note, setting the intonation by fretting the 12th fret brings you the closest you can get to perfect intonation.
 
Another thing, setting intonation is really trying to "divide" the string ever so perfectly the best you can at the 12th fret by moving the bridge saddle forward or back. Now why do you want to do this? The reason you're dividing the string at the 12th fret is the very reason your using the 12th fret harmonics when setting the intonation, BTW back Bach era I think this was called "Well Tempering". 12th fret harmonics are NOT produced by the 12th fret, they're produced because they're dead center of the length of the string from the nut to the bridge saddles, frettless basses can produce a 12th fret harmonic.
 
Most guides to setting intonation (at least the ones I have come across) refer to comparing the 12th fret harmonic to the 12th fretted note. Why? Why not compare the open string note to the 12th fretted?

Because if the saddle is in the wrong place and the intonation is incorrect, the 12th fretted note will be incorrect, too. :smug:
 
Ears are more efficient and attuned to pitch at higher frequencies, if I tune to a guitarist I ask for the open G string (or better still, the harmonic) rather than open E because of that.

When I intone my basses, I'll use a few frets along the strings for reference not just one or two, fretting machines are not perfect.