Contrary to OPs opinion, I believe tooling is relevant to the learning process, because an inconvenient system will put you off from taking notes and from coming back to them in the future. The catch is, there is no single tool that will fit everyone, you have to find your own method. My own tooling choices have changed a lot across the years.
When I began to apply a structured method to my studies, my first choice was to use mind maps. You can structure a mind map to resemble the associations you have in your own (duh) mental model of any body of knowledge you might be studying, and then it's easy to navigate a map with your eyes to recall stuff and fill the gaps when things get cloudy in your head. The first digital tool I recall using was CmapTools, and it's still pretty good.
Nowadays I use mostly LiquidText for reading notes, on books and articles (but there are other similar products). It lets you build something similar to a mind map, and it's really convenient to select a piece of text or image on a pdf and make it a node in a map. It's especially convenient if you have an iPad Pro with a Pencil. However, I could still not find any single tool that encompasses all my "learning modes". For instance, if I am playing with some OSS project and want to take note on something interesting, I have to use a different product.
OP here, if the article seemed to imply that tooling is irrelevant, that was not my intent. The most important part of any system is that it be something you'll stick with. I 100% agree with you that if a system puts you off from taking notes than it's bad for you. (I'd add the nuance that what's off-putting for one person might work well for another)
That said, it's dangerous to let the perfect be the enemy of the good. I'm trying not to spend too much time researching new systems and instead focus on benefiting from the good-enough system I currently have. I moved to my current system when I was feeling the scaling pains of my old one, and when I feel those pains from this system it'll be time to search for an upgrade!
Speaking of upgrades, I don't have a good way to take notes from pdfs. Looking at their site, LiquidText seems like it's optimized for the pdf use case. I'm going to dig deeper into it to see if I can read pdfs and take notes in there, and then export those notes into Evernote. Thanks for the tip!
When I began to apply a structured method to my studies, my first choice was to use mind maps. You can structure a mind map to resemble the associations you have in your own (duh) mental model of any body of knowledge you might be studying, and then it's easy to navigate a map with your eyes to recall stuff and fill the gaps when things get cloudy in your head. The first digital tool I recall using was CmapTools, and it's still pretty good.
Nowadays I use mostly LiquidText for reading notes, on books and articles (but there are other similar products). It lets you build something similar to a mind map, and it's really convenient to select a piece of text or image on a pdf and make it a node in a map. It's especially convenient if you have an iPad Pro with a Pencil. However, I could still not find any single tool that encompasses all my "learning modes". For instance, if I am playing with some OSS project and want to take note on something interesting, I have to use a different product.