Exactly. Personally, I gravitate toward book and topic-specific notes and highlights in the book itself and use the notebook for bigger-picture things for which book references play some role. I do a lot of highlighting in ebooks and lately I've started using LogSeq. I'll pull quotes from books into LogSeq and then tag them with whatever #bigger-picture topic I deem relevant, mimicking what I do on paper.

For my textbooks, I use little record cards. I write the book reference on the top line, then whatever notes or quotations etc. If it's a heavily referred to book, I sometimes use different colour cards to mean different things.

When I return the book to the library etc., I take all my record cards out and put them in a little perspex index box.

Sometimes I use the record cards to then start some more detailed notes in a notebook; sometimes the record cards refer to a page in my notebooks where I've attempted a derivation etc.