Eep, I guess it depends on what kind of learner you are. For me, the notes being in the book, and the book being somewhere on my shelf spatially encodes it into my mind.
Offloading things into a centralized store according to a system not only causes me anxiety but it doesn’t have the same spatial kick.
Reminds me how the original Mac Finder took spatial memory very seriously. Wherever you moved something on the desktop or within a particular folder, it stayed there.
That’s definitely a design principle that’s been long since lost.
I used to take notes on loose sheets of paper, fold them, and stuff them into the book between pages. I guess there are lots of ways to build a system.
A few books I've taken enough notes to collect them in a folder. I put section tabs in the book and tabbed dividers into the folder with matching colors. I note the page numbers for each note. Then I shelve that folder to the right of the book it was noting.
I agree with the spatial memory and the many possible and valid ways to approach reading and learning. But it's much harder to recall, connect and leverage ideas that way