The real problem the designer and the engineering split.
Designers should be fired.
The best apps in history have been built by hackers with a great aesthetic sense.
Somehow we have lost this today.
You could s/Designers/Engineers/ and end up with the same statement.
What you seem to be getting at is "hackers with a great aesthetic sense" - and what makes a hacker, then? An engineering background? A computer science degree? Most designers have some understanding of the platforms they're working with. Could they invert a binary tree on a whiteboard? Write an LRU cache? Scale a system to a million DAU? Usually not, but you don't need to do that to build a proof-of-concept application that people fall in love with.
A designer may be a hacker, just as an engineer may be.
If you go straight into OPs system you'll spend way more time trying to figure out how it works (and it might not even work for you) rather than getting actual work done
Start simple. Write a few notes. Maybe you need to draw things: add Excalidraw. Maybe some note structures are similar: consider Templater.
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.