I'm not certain of what tool he is using to generate the SVG files but a great option is Inkscape, which is FOSS and free-as-in-beer. If you want an illustration tool, Inkscape is definitely the best non-Adobe option I've used (and as someone with a monthly subscription to all of the Adobe tools, probably the best option overall).

IIRC, custom WebGL stuff that he writes himself. So he's a 10x technical writer and a 10x developer.

You can view the source on the page, it's all there.

It's literally in the page JS source.

I don't entirely follow...

Most of the diagrams in this article are SVG files. Yes, you can look at the source (a big pile of numbers), but that doesn't say how they were created.

I realize that a lot of this author's other articles have animated WebGL stuff, and the source code is illuminating, but not so much here, unless I'm missing something.

You are right, my comment applies to other articles by this author but not this one.