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This quote seems to support your claims.
To adjust the intonation of your guitar or bass, you move the bridge saddles toward or away from the fret board until the 12th fret octave and its harmonic are equal and the same open-string note is exactly one octave below those.
On further reading however is this quote...
Adjusting an instrument's intonation consists of setting the bridge saddles to produce the note at the 12th fret exactly an octave higher than that of the open string.
which is the definition I always understood to be correct. No mention of the harmonic.
Further support for this comes from this.
With the aid of an electronic or digital tuner, compare either the open string or the octave harmonic at the 12th fret with the fretted octave at the 12th fret.
Note the either and or. The 12th fret harmonic
should be co-located with the mid point of the string, and usually is. However defects in the string, nut, saddle or pup placement can cause the harmonic to
not coincide with the string mid point.
I therefor stand by my claim that the harmonic is independant of the intonation process. It should coincide with the mid point but may not under some circumstances.