His point is not helped by making false claims such as "Equal temperament actually did not come into use until the 20th century."
More importantly, the idea that Bach's WTC was intended to "demostrate the varying key colors in well tempered tuning as one progresses around the circle of fifths" sounds pretty uncanny when you know some context. As an organist, Bach was used to being heavily restrained in which keys and intervals could be used while dodging the many obstacles that were dissonances in the instrument's tuning.
The purpose of Well temperament, used on the harpsichord, was to get rid of those limitations and gain the ability to transpose everything freely while remaining consonant and in-tune. In this way, the Well temperament can be seen as an approximation of equal temperament in a time when the mathematical tools to achieve it were not really known.
To me, it's pretty clear that the WTC is Bach gleefully exploring the freedom of transposition-invariance and free modulation. In other words: Bach would have loved the equal temperament, and this article would likely give him a hearty chuckle.
I like natural intervals, but dividing the octave in 12 tones is a rather inappropriate way of using them. European classical music adopted this system early on, and therefore was doomed to end up on the equal temperament at some point. It's not the ultimate system nor the end of temperaments, but it's been really, really useful.