> People should start using these apps as simple note-taking apps and extend/adapt them based on their needs
This. I'm a hardcore Obsidian user both at work and at home, and I started both vaults from absolutely nothing - no user scripts, no organisation, literally no plan at all. Since then, they've evolved and optimized in radically different ways. Taking someone else's "system" is just a way to fool yourself into thinking you can be more productive than you are; you have to find that for yourself and what works specifically for you.
My personal vault is geared much more toward organizing creativity, with a little bit of task-oriented stuff and technical documentation, while my corporate vault is heavily schedule based and contains mostly tactical information, meeting notes and thoughts, etc. For it to be a "second brain", you need it to model your brain - and I work very modally. I have a "work mode" and a "non-work mode" that order things pretty differently, and it shows in the hierarchies and organization of both vaults.