Intonation - the 12th Fret Harmonic vs. the Open String

The question I tried to answer today is, "Which is more better?"

• Comparing the note at the 12th fret with the harmonic at the 12th fret, or
• Comparing the note at the 12th fret with the open string

Today I set the intonation on my new guitar for the Xth time.  I have a Peterson Strobostomp, which is good because neither my ear, nor a needle tuner, has ever helped me intonate a guitar.  And I couldn't tell see much difference between the two methods.  I think the reason is that if the intonation is already close, the harmonic and the open string are converging somewhat.  Who knows?  It's such an inexact thing.  My favorite E-form barre chord sometimes sounds good to me, and sometimes sounds horrible, when played up the neck.  That can change from day to day.

I tried hacking the G string compensation a little by increasing it arbitrarily, because it seems like the G is the primary culprit in spoiling my perfect chord.  I've heard of studio musicians doing that when they know exactly what intervals, and where on the neck, they're planning to be.  I think experienced luthiers, guitar techs and musicians consciously or unconsciously "sweeten" their intonation, and they're not telling me how it's done.  I've read that experience musicians of the fretless persuasion (eg violin) adjust their intonation dynamically, like magicians.  

I'm trying to work up a system for hacking intonation that works reliably, and when I do, I'll post it.  It'll be something along the lines of:

1. Play your chord or group of notes where it needs to be
2. Strum repeatedly and silence different strings in turn, looking for the one that's ruining it most for everybody
3. Use the regular guitar tuners to nudge that string up or down a little at a time (basically make it out of tune) until it plays better with others
4. If you sharpened it, decrease compensation for that string beyond what is normal, and if you flatted it increase compensation beyond what is normal

Also I just realized that I might be able to do something using just the tuner:  hold the chord up where I need it and, in effect, see how far from equal temperament perfection each note is.  That's basically simple intonation, but maybe it changes the equation when all the strings are fingered?

I am a monkey.