I've taken 3000 pages of notes in a linear, bullet-point fashion, and I also keep up with education research. As far as I can tell, both in studies and in personal experience, the fiddly details of your note-taking schemes don't matter. The only thing that matters is attempting to integrate the information into a cohesive whole, which takes intentional thought. With linear notes, there's a failure mode where links th…
For linear notes, the remedy is not really feasible, you'd have to go through everything thoroughly fixing unlinked notes.
For the 2nd, the 'failure mode' of the web note taker as you describe, that isn't really a problem. Notes are just tools/building blocks to writing or coming up with cohesive ideas/arguments. If you don't know what Y was for, its either irrelevant or you've found a gap in your knowledge you need to plug.