That’s a fair point. But still, the relationship between the root, 5th, and major third are very much connected to the fact that they are specific multiples of that root frequency, and are the loudest overtones typically audible when the note is played. The root is not totally different from chords built on it.
I meant to add more to my top comment. I think the author does fairly well at their mission despite potential nit picks like that. It is really cool to see somebody learning and being excited about putting all the pieces together. The beautiful thing about music is you can go deeper and deeper as much as you want, and there are various competing ideas about what it is and how to talk about. Programming has a similar kind of depth to it.
depends on the instrument. A pure sine wave at the frequency of C does not have any overtone.