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I have played around with my intonation, and while its not perfect, its only 3-4 cents off in most places, sometimes it will come really close in others.
A perfectly tuned guitar, playing a simple 5 chord with distortion, sounds like a small oscillation effect (like a rotary, without the stereo pan) since the frequencies are "rubbing".
Also, dont forget that everything will be a little distorted since it is coming from a speaker instead (limited polyphony technically) versus acoustically (ulimited within the instruments range/playing ability). Some of that may be what you are hearing as well.
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