The "fooling themselves" element is in thinking adding sophistication beyond two those things improves the usefulness of the notes themselves. And there's some personal flexibility here too sure; if you truly can't ever find a note when you need it and adding a tagging system gets you there then that's useful additional sophistication.
I think the point they were trying to make, definitely the one I'm making, is that the line between useful system and hobbyist tinkering is a lot lower than people want to think, because they want to ascribe purpose or benefits to their tinkering. Which is where the productivity porn comes in, a framework that only values things if they are or contribute to "productivity" demands everything be productive, demands that you justify it.
But truly and honestly if you have a flat folder of text files and grep you have what you need and beyond that is tinkering. That's what people are fooling themselves about.
I built my own "digital notebook" and use it literally every single day for almost everything I do. When I'm in the middle of a project, I use it to take notes, write down questions, organize my thoughts, and save useful web links. It's hard for me to overstate how critical this to is to my day-to-day life. My notes ARE the thing I need most in order to "just get shit done."
Yes, there are "tool fetishists" in this space, just like you'll find in any career or hobby. They get their enjoyment out of tinkering with these apps and cataloging the hell out of their notes. I'm not one of those which is why my app has practically no curation abilities. But I also think it's in extremely bad taste to shame those who apparently enjoy it.