>Maintaining notes separately breaks the flow of reading.
I would push back on this point. You do not have to keep a flow of reading. If there is something that stands out to you, then it is noteworthy enough to pause and think about it for a bit. When I read books I am waiting for moments like this, as something the author wrote resonates with me. In my opinion, that's what makes reading fun and valuable. After you reflect on the line you can re-read to get back into the flow until you are pleasantly provoked by the next piece :).