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So the author is keeping notes in a flat hierarchy and then using the graph.

He stated that the goal is "greater understanding," and then he just (in all honesty) states that the nice graphical topology represents my learning journey and keeps me motivated.

That is exactly the problem: motivation and a history of learning do not always lead to "greater understanding." On the contrary, I find that our 'notes' are often transient while our internal understanding morphs subtly yet swiftly (especially when learning something new).

That is why I think 'organic linking' works better for very large AND more definitive content. Wikipedia is the best example.

For personal use, I prefer more structure. The outliner/database combo (like logseq) is the best tool for that.

And Frankly as long as I can easily download my data in a readable format, I'm OK with any tool. It does not have to be built as plain text files.

But I do like Obsidian :)

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I often hear of people using Obsidian or other feature-ful not taking and task organization apps creating PKMS (personal knowledge management systems) in then. They often state that linking things together, categorizing and organizing them well, and using appropriate tools to help view these associations that it results in... "realizations", or "understandings"? But I've yet to see anyone mention a concrete example of what they mean by this.

I can use my imagination to come up with some potential examples, but I'm curious these conclusions actually often occur or if people are just chasing some idea, when in reality they just get enjoyment from the organization process.

Either way, I use Obsidian lightly and am trying to refine how I use it, but I'm definitely not "there" yet. I mostly enjoy having a personal wiki basically of any information that I've researched or need to keep on hand somewhere. Main downside I've run into is that I'm not a huge fan of the layout / UI (maybe there's plugins for that) and tables are horrendous in it (I know they just added an update for them recently but I've already offloaded my table-style data elsewhere and I don't plan on bringing it back).