The SG and the Taylor - I have had for a few years - and have been professionally set up multiple times over the years.
I record to midi and tuning is very important to me. When I fret a note - I expect it to be in perfect tune.

With all of my guitars - however - they do not play perfect notes when fretted. Some fretted locations are perfect tune - some not.
String Guitar Tuning: The Ultimate Guide
With all 3 guitars - particularly when fretting the A on the G string (3rd string 2nd fret) - the A always is sharp somewhat.
For the Taylor and the SG - if I compensate somewhat on the G string, pulling it back - not quite flat - the A will then be close or spot on when fretted.
I have a Epiphone Studio - does the same thing... but for $400... Why am I spending thousands of dollars to have guitars that do not fully tune?
How To Tune A Guitar Without A Tuner
I have these discussions with the sales reps at the Guitar store - they say it is in my head or Supposed to be that way. I feel they are sales motivated and will stray from the truth.
I have played guitar for decades - it is not a fretting issue (how I fret the string). I have tested various fretting techniques and use a consistent fretting method - to test the tune - to ensure the data is the same.
Not sure this is an answer to your question, but if your ear likes just intonation (no beats in chords, ) you're going to have trouble with playing in different keys. If I'm playing a 6th-to-D piece on my classical guitar, I tune it so all the D chords are in tune with each other. Some of the other chords then are not. In a different key I'll tune the guitar differently. Since I play classical, my commentary might not apply to the type of you play.
What Is The Logic Behind The Fifth Fret Method And The Harmonics Method Of Tuning A Guitar?
Without seeing them, and setting them up again, to my satisfaction, it's difficult to tell. One thought is that you are pressing down too hard, making things out of tune. On a properly set up instrument, there should be no need to press the strings into the fretboard. We've all been there, and wonder why the callouses grow. Pressing more gently, but still achieving clear notes is all that's required. Haven't seen you play, obviously, but that's one idea.
Have you checked intonation at 12th and 19th frets? If the guitars have had 'multiple set-ups', I wonder why you felt that was necessary. Changing string gauges often, will make a check a good idea,
EDIT: You could try a different sort of intonation check. Open string harmonic at 12 gives same pitch as fretting 12. We know that. But - try fretting 1, harmonic at 13 should be the same as fretted 13. Same for all - fret 2, harm. on 14, same as fretted 14. This MAY point out discrepancies with fretwires, but more likely will show the frets are o.k.

List Of Guitar Tunings
It isn't mathematically possible for a guitar with straight frets to have perfect intonation. See this thread, particularly #6, for further explanation: https://www.seymourduncan.com/forum/showthread.php?282597-do-any-of-your-guitars-have-perfect-intonation
You can maybe get them setup using the PLEK system which claims to improve intonation. Echoing @dissemin8or you are probably expecting too much from a standard setup
It could be due to a slipped bridge (in the case of a floating bridge) that can simply be realigned, or, if it can be raised and lowered as in the Tune-o-Matic design, to the need to try that- or to the need, possibly, to adjust the neck truss rod, which in the case of an expensive guitar I would get done by a technician. If the problem is persistent, you can get it refretted or failing that, sell the guitar on to a tone-deaf person. A final thought, guitars are temperature and humidity-sensitive and maybe they're just not happy where they are? Just suggestin'.Why you sound out of tune often depends on your level of experience. Beginners, for example, sound out of tune because they tend to tug at the strings pulling them sharp. A perfectly tuned guitar can yield chords that sound disonnent because of poor technique.
The Guitar Fretboard Notes
Intermediate and advanced guitarist sound out of tune for different reasons. Number one, even a perfectly tuned guitar is slightly out of tune due to design. By that, I mean there are basic flaws that even under perfect conditions some notes will be slightly out of tune.
In the original version of the course I explained, “Changing strings isn’t like changing the oil in your car, it won’t make your guitar last longer. You won’t damage your guitar by not changing strings.” Still, there are advantages to new strings – they’re brighter sounding and can cause a guitar to sound in tune (guitar intonation) with less dissonance.
Have you ever noticed that some chords and notes sound out of tune on your guitar while others sound perfect? For example the open A minor chord might sound in perfect tune but the D barre chord at the fifth fret may sound dissonant. You can actually tune the individual strings to make the D barre chord sound perfect which will cause other chords to sound dissonant. This is caused by notes at the twelfth fret and beyond being out of tune when the open strings are tuned to pitch. What’s happening is, high frequency overtones aren’t in tune and these overtones occur even when playing open chords. The cure – adjust your guitar so the notes at the twelfth fret are tuned to the exact same pitch as the open strings. This is accomplished by adjusting the intonation.
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When the guitar intonation is properly adjusted all notes will be in tune or at least very close. Do to the physical construction of the guitar it will never be in perfect tune but the idea is to get it as close to perfect as possible.
To tune the twelfth fret to the open string you must slightly lengthen or shorten the string. If the twelfth fret is a little sharp, the string needs lengthened to flatten the pitch at the twelfth. Conversely, if the note is flat, the string needs shortened. It’s safe to assume that the intonation on your guitar was set properly at the factory or by your local guitar tech. Over time the neck moves causing notes at the twelfth fret to become a little sharp or flat. Use a digital tuner to tune the open strings to pitch. Now check the tuning of notes at the twelfth fret and higher. You’ll probably notice that all are a little sharp or all are a little flat.
Here’s why. There is a constant tug of war between the strings and the truss rod, the bar that runs through the middle of the neck to protect the neck from becoming warped. The tension of the strings pull the headstock towards the bridge. This bows the neck causing a gap between the fretboard and strings. This bow actually shortens the strings causing notes high up the fretboard to sound sharp. The truss rod bends the neck in the opposite direction to counteract this pull from the strings. Tightening the truss rod effectively lengthens the strings. So when the truss rod overpowers the pull of the strings, notes at the twelfth fret become flat because the strings are lengthened.
How To Tune An Electric Guitar
It’s beyond the scope of these instructions to explain exactly how to adjust the intonation on your guitar but this information is easy to find on the Internet, from your guitar’s manufacturer, or from our Guitar Setup and Repair program. I’m just going to explain the basic process of intonating a guitar without explaining the mechanics of adjusting different models.

First, put new strings on your guitar before doing any intonation adjustments. Strings affect intonation in many ways. For example, if you change the gauge of the string intonation is affected. As strings age the intonation changes so it’s important to make these adjustments using new strings. After making these adjustments you probably won’t need to do this again for several months if you continue to use the same gauge and brand of strings.
When you change the strings replace them one at a time. If you remove all of the strings at once it will take a few days for the neck and bridge to return to a normal position. After replacing the strings, wait a day or two before making any adjustments. It takes time for the neck and truss rod to settle down after a string change. So, two or three days after replacing the strings tune the open strings to pitch and check the tuning at the twelfth fret and beyond. You’ll notice one of three things: 1) All notes will be flat. 2) All notes will be sharp. 3) All notes will be roughly in tune with some strings sharp while others are flat. For number 3, move on to bridge adjustments because your truss rod is adjusted properly.
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If the
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