Paper and digital note systems are not in conflict. When I'm working through the math in a paper, I'm not going to type 50 lines of equations into a text editor. I take a picture of my notes, upload it to OneNote, and copy the link into my text notes on the paper. It's surprising, but you can have a 100% digital note system while using paper for 90% of your notetaking.
For years I took notes both with pen/paper and digitally, and either cross-referenced things or scanned pages into a master digital document like you describe. For me, the game-changer has been getting a RocketBook. It’s handwriting recognition is about 98% accurate for me, so it only takes a few minutes for me to scan some pages, drag the emailed text file into VS Code, join lines into paragraphs, and check for typos. Gives me a chance to review what I wrote too. Then it goes from there into a plain text file (or more recently, WorkFlowy) which is my preferred system. I started with the free PDFs that RocketBook makes available, but finally bought one mostly because I wanted to pay for their server resources. :-)
The RocketBook is actually what got me started on this. My pen died, so I started using the OneNote app (service provided by my employer) and it's worked well enough. I definitely recommend the RocketBook.
