Some further thoughts on ephemeral versus preserve-everything note-taking.
Note-taking is about capturing ideas, thoughts, and processes. You want as little friction as possible when doing so: you don't want to be thinking the page is too small, or the paper drying up the ink too quickly so the pen doesn't move smoothly, or similar such things distracting from capturing what you are trying to capture.
I used my PhD notebook as an example of a preserve-everything approach. A serious drawback of the notebook as the sole place to capture work is the risk that it will be damaged or lost. I periodically photograph all the pages and store those photos digitally, alongside other things relating to the work. Those other things include two different private wiki instances that I use to capture notes when I'm working at the computer, as well as several Git repositories (some public, some private) for source code, experiments, drafts of papers, etc. There's also a not-insignificant amount of email correspondence.
There have been several train journeys and several meetings where I've grabbed a cheap, larger-format pad of paper and a box of Pound-shop felt-tip pens to sketch ideas, whiteboard-style. At the time it just seemed easier to capture what we were doing in that way, rather than try to do so into the notebook.
So the notebook is neither canonical nor comprehensive. Ultimately it's really another example of ephemeral note-taking, and so I think the Ephemeral model wins out.
Use whatever notebook or paper or envelope or window pane that is convenient and feels attractive at the time you need to capture something with the least amount of friction. Digitise that and store, catalogue, adjust, derive, etc. from that in the digital domain.