Earlier quoted context omitted.
The key to the article, and to all of Western music, is about a set of weird mathematical coincidences involving the twelfth root of two. In particular, that twelfth-root-of-two to the fourth power is almost exactly 4/3, and twelfth-root-of-two to the fifth power is is almost exactly 3/2. And, of course, twelfth-root-of-two to the 12th power is exactly 1. For some reason, not entirely well understood, when you play f…
I think you're maybe missing the main motivation, which is that "correctly tuned" overtones are in nature, in physics, in all sounds -- they aren't a social construct, unlike everything else about music. I think the argument from JI advocates is that our body's perception knows very well what a justly-tuned chord sounds like, etc.
The idea of the harmonic series is a useful approximation, not a physical truth. Fourier applies to completely static waveforms, and says nothing about how waveforms change over time. If you try use Fourier for dynamic waveforms - which is most of them - you run into all kinds of problems and tradeoffs.
So the concept of whole number consonant ratios is an attempt to impose a mathematical ideal of perfection where it very much doesn't exist.
Clearly music is related to the harmonic series, but it's related around it, not trapped inside it. The dissonances and deviations create colour, tension, and movement.
This doesn't mean xenharmonic experiments aren't worth doing, and we should all just use 12TET and not think about anything else.
But it does mean these are experiments away from real acoustics into computed perfection, not back towards a perfect ratio heaven that music was exiled from by 12TET.