Even your fancy guitar is not exempt from harmonics math. TFA has nothing to do with the quality of a guitar and everything to do with 12-Tone Equal Temperament.
Weird to describe 99%+ of all guitars, including some of the best made guitars in the world, as "poorly made."
This article is relevant to a theoretic perfectly designed and built guitar.
You’re assuming that the goal for a guitar player is to have perfectly optimal instrument when in reality many players want an instrument that feels and sounds like the artists that inspire them. Aesthetics is part of that but if they enjoy the sound of the instrument then who’s to say that another one is “better”?
The most guitars today are still made in the style of the 1950s Gibsons and Fenders, including the neck and tuner layout. Most guitar buyers focus on the aesthetic and not the quality. I switched to a headless guitar where the tuners are at the bridge and it has a fanned fretboard giving the strings more natural tensions, the thing stays in tune and is intonated at the frets extremely well.