I can't comment regarding how you think is best to teach your students. This is now a popular blog post that has gone viral on HackerNews to a much wider audience of well-educated people, so you should expect people will clarify these things on here. I'm talking mostly about stuff like this:
> Five hundred years ago, however, it would have made a very big difference. Before the advent of temperament systems, D-sharp and E-flat were two different notes. They weren’t just written differently; they sounded different. You can compare the historical versions of these notes yourself in this track I made... My track is tuned in a system called five-limit just intonation
^ These are not the historical versions of those notes. 5-limit just intonation was not in widespread use in Western Europe 500 years ago. 500 years is not before the advent of temperament systems. And so on. Teach this to your students however you think is best, but people on here may be interested to know that.