Interesting. That's pretty much how my own toolbox has evolved as well, though I wasn't really aware of it before reading this essay!
My tech stack is Emacs plus a few add-ons (org, org-roam, notmuch). I have an org-roam database for long-term notes, and two plain org files (work/personal) for short-time notes and to-dos. A crucial feature for me is that I can link from those two org files to my long-term notes, to e-mails, and to the individual files and directories in which I manage larger projects, in particular collaborative ones. Each project also has an org file for project-specific short-term notes, for the notes I share with my collaborators.