The most effective use of taking notes is to actively engage with the content by figuring out how to organize it and what to include and what to leave out. Even though the author says to just capture everything, if you are doing it by hand, you are making decisions on what to write and what to skip simply because you can't write as fast as someone talks. One of the reasons taking notes on a computer isn't as good for retaining information is because you CAN probably keep up with how fast a professor talks and capture everything--so you don't end up actively thinking about what is being said.
This is a great use in the short-term. In the long term, you also need situations where you will apply directly the contents of your note. You can explain the subject to your friends or co-workers, use it as the basis for research that you are yourself doing, or synthesize what you've written down with knowledge coming from other books. This will keep you coming back to your notes, and you'll feel that your knowledge is increasing and getting sharper each time.
Exactly this. Focusing not just on what you write, but how you find what you wrote is very important.
I started using Org Roam a bit over half a year ago. My policy with deciding what to store in it is: "is there a chance I will want to remember this later?" If yes, I write it down, and link it to something relevant, which allows me to find it later from the backlinks on that relevant note. I thought I had pretty good memory (I still think it isn't bad for a normal human) but I have been surprised fairly often that some tidbit of information that I want is neatly available as an atomic note, and I don't even remember writing it.