|Jim S.||Intonating by ear|
"for intonating guitars I get as close as I can with a tuner and fine tune by ear"
I agree 100%! To get a guitar to sound really ON, intonating by ear is the only way to go. Merely intonating by comparing fretted (12th fret) to harmonic octaves only gets you just inside the ballpark. There is no such thing as a perfectly intonated guitar. It's all a matter of reaching the best compromise.
If your ear is good enough that you are unhappy with the way your guitar sounds when intonated using the 12th fret octave, then its good enough for you to use it to fine-tune the intonation.