Practical example? You can be annotating a PDF, while having executable code blocks in different languages, e.g., you can run http or sql query, then pass the results into a python, javascript or shell scripting block, and then output the final result into a diagram. So, you'd be reading the book, taking notes and mess around with practical code snippets at the same time.
I have tried so many different note-taking apps, philosophies and techniques over the years. Nothing even comes close to what I can do today in Org-mode. It totally shatters everything else and kicks the shit out of the ballpark.
I'll just say that even to another "expert", you didn't explain what's so great about this annotation workflow.
As for the annotation workflow, well, I guess you just don't need it. When you decide to start writing notes while reading books, I'm sure you'll be able to figure it out. For now, just create a TODO item with a deadline, it will keep showing up in the Agenda, but I don't have to explain, that part you know already.