This doesn't really explain any of the music theory that's described on the linked page, unless you're meaning you're explaining a theoretical basis for harmony itself? The kind of music theory on the page is about triadic harmony, scales, the ways in which one triad moves to the next, non-chord tones, melody, and rhythm.
I do like thinking about tuning systems, however.
- If you have purely harmonic instruments, like bowed strings or the human voice (due to mode locking), there's some justification to try messing around with extended just intonation systems (ones where the ratios use prime factors that go beyond 2, 3, and 5). Ben Johnston has a workable notation for this. But, even after having played around with this for a while, I still struggle to hear things involving 7 or 11 as being in tune!
- For slightly inharmonic instruments, like pianos or plucked strings, just intonation seems to make a bit less sense... though La Monte Young's "The Well-Tuned Piano" with it's 2,3,7-based tuning does work pretty well. (And as someone else pointed out, piano tuners compensate for inharmonicity even for 12-EDO tuning by making all the intervals just a bit wider. So twelfth roots of two don't completely explain things.)
- I'd be interested in seeing how highly inharmonic instruments, like bells, might be tuned to take advantage of their own unique harmonies. It might be that a "5/4" ratio means "take the fifth harmonic of this bell, then find a bell for which that harmonic is the 4th harmonic."
Equal temperament, by the way, apparently wasn't popular until around 1900-ish, and so-called equal temperaments before that tended to be various kinds of unequal but "circular" temperaments that worked well enough for every key, yet still preferred common keys. See [1].
12-tones is an approximation of tuning systems that had been long used by singers and string players. A C# is slightly lower in pitch than a Db (in cents, this is roughly 87 cents vs 109 cents; musicians should be able to perceive deviations of 5 cents, for comparison). In fact, there were early experiments in having split black keys to be able to have both pitches on a keyboard. In [1], the author argues that 1/6-comma meantone is a good approximation for this system, which can be explained as 55-EDO. This makes sweeter major thirds (closer to 5/4 than 12-EDO's 81/64) at the expense of more dissonant perfect fifths, which tends to work out OK for post-medieval western harmonic practice.
[1] Ross Duffin, "How Equal Temperament Ruined Harmony"