How often have you finished a book only to retain the vaguest sense of what you just read?
This is anecdotally a pretty common occurrence, and I've found that my recall improves when I introduce a few additional practices:
Engage my own critical thinking. "Is this a good idea?" "What are arguments against this?" "How would I articulate this to someone else?" Basically, anything that forces my mind to actually work with the idea, instead of just passively absorbing.
Externalize complex ideas. For multi-step arguments that exceed my working memory, I write down the components and work through them independently.
With that in mind, this is how I use my PKB to read (mostly non-fiction) books:
I read a book once through to get the overall picture.
I create a textfile with the name of the book in my Reading/ folder.
I take another pass through the book and try to extract all the ideas or facts that I find interesting. Even if you disagree with it, it's often worth recording to sharpen why you disagree with it.
I annotate these notes with my own thoughts and commentary.
I then cascade the interesting insights from the notes about this book through the rest of my PKB. For example, if I just read Seeing Like A State, then I probably have interesting ideas to cascade to my PoliticalScience/ folder.