I only read on a kindle, so obviously the marginalia system is out of question. Here’s what I do: I highlight the passage, write a note where I summarize it with my own words. That’s all. But I also have a (physical) notebook where I write using the Feynman technique. On top of it all, I read at least 1 hour a day where I’m fully focused (or at least at 80% capacity) and you know what ? Good shit sticks: I trust my brain to capture what it deems valuable. If I forget something I don’t sweat it, it’s more likely that I don’t need it.
I agree and also if I read similar concept in other book, even if I did not "remember it", I feel often dots connecting somehow in my brain and "ahh I just read that in other book". So it is more like gathering concepts than explicitly remembering that concept so I can quote it back when woke up past midnight.
If someone wants to quote book from his head go for Anki and drill, most of books I just want to internalize concepts.