and i think that is partial evidence of my point. as important as being in tune is what are you attemping to tune too? even temper sounds less than perfect and thats what guitar necks are designed to be though stretch is easy enough to intonate in, uneven temper would require squigly frets and make music less transposable and alternate tunings a mess. there have been many attempts at alternate temperments on pianos but it's difficult to apply to guitars. fretless strings can adjust to the players ears and horns dont have as many upper harmonics and dont have harmonic stretch like strings that i know of and i dont think they play chords either so imperfections aren't as apparent.
our brains are interesting in that they like order. low numeric value whole number ratios. which is impossible to acheive in a way that can be transposed or used in multiple keys without compromises. we try to keep it to compromises our brains don't dislike as much. also the right type of disorder in the right places can make stuff more interesting. i mean who wants to listen to all major scale music all the time?
an out of tune instrument sounds bad because the notes dont harmonize and the phase relationship changes causing pulses or "beats" in the chords but the beats change with the chords. but at the same time if the frequency or phase or amplitude of the base notes is shifting at a regular rate as in the case of phasers, flangers, chorus, vibratos, and tremolos or any other modulation, delay or reverb effects it hides poor harmony and we accept and welcome the caos as if enough layers of complexity eventually distract our brains from the slightly off ratios or something. clipping (overdrive/distortion) also adds some musical value in that it creates even order harmonics. overdrive also adds some compression to hide sloppy playing.
all i know is the more scientific you get about intonation the more it will frustrate you. anyone who has been pleased with compensated nuts and other fancy gadgets usually tries and decides that it is more pleasing or not rather than systematically looking for unharmonious chords and getting obsessive over intonation, the decision is ussually made in a few strums of some chords often on acoustic guitars without adjustable intonation. earvana nuts change the temperment mostly of the open chords and it either sounds more pleasing to the player or it doesn't. sometimes it's placebo, sometimes it's preference, there is certainly a difference but i think if you listen to one way or another you eventually adapt. i've even seen an article where an editor goes into intonation a vintage telecaster and by the time he got something he liked he wound up intentionally setting his 6 saddle guitar bridges the same way because of how the poor intonation helped with certain chords and he liked the overall compromise better which is in line with swarfrat's tounge in cheek comment. im not saying either is right or wrong but there is a market for both the traditional and the "correct" way and neither is perfect because music isn't perfect..
