All digital note apps have the problem of making me work very hard to fit my thought into their "organization" of things: hyperlinks, a list of some arbitrary order, a tree, synchronization quirks, and whatever.
It's very painful to work outside their envisioned use cases.
For instance, most open-source solutions focus on a plain text, and if I do use plain text, they are reasonably good. They problem is I need more than that. I need diagrams and tables. Tables written with ascii characters are really hard to maintain.
In the end, I went back to a notebook, and occasionally a stack of sticky memos when I need to clean up some disorganized thoughts. The benefit of the physical world is the freedom of doing whatever I want to the medium: ordering, clustering, rotating, clipping, pasting, etc.
I guess that the digital user experience just isn't there yet.
My go to is goodnotes on an iPad Pro with Apple Pencil. Has a desktop app for macos as well. Literally I haven’t touched a physical notepad since. It is always ready, expressive and just works. Plus I can split screen with PCalc to crunch some numbers.
I wonder if you could get part of the way there by having an iPad or remarkable tablet that is just always on and charged ready to take notes.