The first thing to understand is that there are different kinds of reading. We read for escape, to be generally and specifically informed, to determine actions, and for many other nuanced reasons. I don’t mark up print books- it’s something deeply ingrained. However, most of my reading is digital, and I can highlight and copy passages. I have a medium-size collection of meaningful quotes I have gathered, but it‘s not something I want to manage or optimize. When reading for information or action, I have a core group of tools I like which support Markdown, such as Omnivore. The point in these cases is usually to extract and organize information, which I do for both reference and project support. I also have a queue for professional reading, and my book club is also a monthly queue. Not exactly answering your question, but it‘s how I approach reading.