I've looked at this one before, but what it is doing is dealing with this guitar, it's fixing this guitar's flaws by doing this… but applying those fixes to another guitar doesn't make any sense
It's not the guitar's "flaws." "Sweetened tunings" have to do with the way we delineate what each note's frequency should be, based on
equal temperament tuning. It's not a perfect system, but neither is
just intonation. It's not possible to build a guitar in which every fretted note will be the exact correct pitch, and when you tune the open strings to be exact, the chords you play will be "off" slightly. Sweetened tunings work to find a compromise in which all the chords will be as close as possible to sounding as good as can be.
For example, if you tune your guitar so that each note of an open E chord are
harmonically correct, in which the 3rd and the 5th are
ratios of the frequency of the root note, that chord will sound perfect. But then play an open D or G or C, and the notes are now off. Equal temperament works to make each frequency an equal proportion higher than the starting tone (e.g., A-440), but again, using those frequencies for the notes in a chord, and they're not perfect. It's simply a product of physics. Sweetened tunings take it one step further, to help make chords sound, as an average, closer than they may be otherwise.
That's the best I can explain it, but that's the gist of it.
Now that being said, I think what the OP is saying is if you have the tuner set to use offsets (which I do), when the open string is showing to be perfectly in tune to that offset, the 12th fret harmonic is not. I checked it, and that's what I found. We know the 12th fret harmonic
is the exact same pitch, along with the octave, as the open note, but the tuner didn't show this.