I find the discussion of these particular use cases both interesting and useful. For myself, I’m dealing with large numbers of PDFs and word documents. These are articles from the medical and neuroscience literature plus documents like clinical trial protocols and investigator brochures describing what’s known about experimental drugs. The scientific literature is brought in through Mendeley but indexed in Devonthink. It mimics my old paper copies and folder structure I started with almost 40 years ago when I began my PhD research. Except its instantantly accessible, searchable, linkable and all lives on the SSD of a 2.5 pound MacBook Pro.
I don’t get along with PDF annotations, just like I never write in books or on printed papers. My notebook is in a Tinderbox file for the project. My drafts are always in some other program depending on where they are headed. Mostly because I try to keep a flow from note to finished writing going one way. Notes are for me, writing is for others.