I'm also not sure if I fully get what the author is going on about, but at least part of it seems to be "don't over-taxonomize and over-architect your note-taking and knowledge management systems, locking yourself into an inflexible format/schema too early just kills it in the long run."

If I'm correct that that's part of the thrust of the article (and I may not be), then I definitely agree with the author. The first time I tried to use Obsidian I burned out because I went all-in on the bi-di linking, tagging, knowledge graph, etc., and it quickly killed my motivation. Now I just dump text in and rely on search to find what I need, only adding links in retrospect once they are needed, and now I actually use it and get value from it.