Physical pen and paper is not for me.
Anyway, I found a candidate: MyLifeOrganized
It ticks many of the boxes, it's configurable more than typical (but not fully), and it's oldschool in development philosophy and design.
It's also missing a feature or two, is a little messy in some usage and visual aspects, and there are a handful non-critical yet annoying bugs/features. Not sure what happens when the trial period ends, but it's relatively expensive as far as general software goes.
While on the hunt I also tried the desktop versions of multiple subscription-based web apps, to see if by chance they can be of any use. They're built eerily similar. All Electron crap, all install automatically or by default into %LOCALAPPDATA% like Vista was just released, and all but one showed just an empty window because the possibility of no internet access is so perplexingly alien.