This is really interesting (I remember reading it years ago), but does not, in fact, explain harmony. There is no explanation of why particular harmonies work that generalizes, nor any methods given for calculating harmonies de novo.

That article is one of the most deeply disappointing to me - even as a composer who doesn't like traditional music theory. It starts with some criticism of traditional music theory I agree with, then goes and... reconstructs several aspects of traditional music theory anyway. Also has a common case of worship of the harmonic series but then conveniently stopping at stuff like 7:4, 7:5, and 7:6 ratios.

I don’t agree. It doesn’t try to refute traditional music theory, but explain why it works.