I understand what you mean about desktopware. OneNote is definitely overkill for what I
really want and I've been thinking about how to get away from it for a long time for several reasons. Trouble has always been that nothing else does all the things it does to my liking and the issues it creates are fairly easy to workaround.
There are some very versatile programmer's editors that I've flirted with as replacements. My guess is that if I ever find something with the sort of project management ui I'm inclined towards, exporting the project in order to a single file for processing will be the easy part.
I was thinking things through as I wrote, and I guess the answer is probably no, though I certainly sympathize with some of your motives. I've done project management manually through file managers with a minimalist text editor before and I really don't want to go back there. OneNote's structural elegance has ruined a lot of other implementations for me.
Not trying to dump on your idea though. Hopefully the feedback is helpful in some way.