Take notes with Apple Pencil on a ePub book?

I read ePub books on Apple Books on my Mac or iPad. I hate that I have to take notes in a separate notebook while iPad’s pencil is so great, and taking notes as annotations on the book itself would be so much more intuitive and useful. Anybody here have any solutions for this? Any app that solves this problem creatively by automagically converting ePub to something else?