I do also live in my note taking app, Bear, and I tried a similar system with bookmarks: I was using Pinboard and set up automation to ingest bookmarks into Bear directly. It didn't work out because 1) too clunky, too many moving parts 2) automation was removing ME from the process, I was not able to "curate".
What I do now is just dropping relevant links in my notes, creating new ones when needed. It's dead simple and ugly and yet works way better than any other bookmarking system I tried.
Creating notes from ebooks is definitely more complicated, because we are constrained by the Kindle interface. I have yet to try connecting the highlights to my notes, thanks for the inspiration!