I am an avid obsidian user and can identify with this use case. I use 4x6 index cards as bookmarks, and I write my notes on those. Then when I'm done I transcribe them.

epub can absolutely be held in a sovereign way. I just happen to have problems retaining information read from ebooks. there's something about the physical instantiation of the book that helps my brain index into it. When I recall something, a passage or whatever, I usually have a sense for physically where it was located in the book. That is, left or right side of the fold, towards the front, middle, or back of the book. upper middle or lower part of the page.