I've started pasting blog posts I really like into Nomad Hypertext, which is cool because I can later see how things I write relate to blog posts I've written
The main challenges are chunking the text so that the paragraphs actually encapsulate a concrete idea, so that the connections between them are valuable.
Hm, I've found it much more useful for journaling and ideation than for notetaking (and I've found this to be true for other tools for thought like Roam/Obsidian as well).
I generally don't take notes when trying to learn something, I usually like to be more hands on (by doing problems, making a project applying the principles, etc.) When I write it's usually to reflect, or to hash out a more open ended problem.