Secondly, from my position as a tech writer (for about 25 years) overlapping for well over a decade with some 20-odd years as a software tech support person and trainer, I think you are dramatically over-estimating the level of understanding of the average Linux user.
A Linux user can be expected to be a bit more clueful than a Windows user, but not much. They probably understand the concept of a "directory tree" and know that there are "files", some "executable", in "directories", one of which is "current", and stuff like that, but you can not rely on them grasping advanced concepts such as "search paths" and "links" (of different kinds, no less!)
The idea that there's a second, "more standard" tree, and it's optionally overlayed on top of the flat software-managed Nix tree, made up of symbolic links, and that you don't need to know where things are because the software magically makes sure that the OS can find them... I'm sorry but after coming up on 40 years in tech, my reaction to that might be captured by the crying-laughing emoticon. You could no more explain that to the average distro-hopper than you could explain it to a Labrador dog.
How it gets set? Don't care. A script is what I'd assume, sure, but that's no more important than the colour of the script's author's hair.
I'm saying that, professionally, as a writer, I have now presented the concept to smart interested users that they let go of the filesystem hierarchy and just let the OS manage that, and I'd say about 9 out 10 of my readers responded "oh to h3ll with that! No WAY!"
It is a step _much_ too far. It's comparable but worse than self-driving cars to these folks.
To refer to memes again, you need the god-level intellect step of the intelligence meme: https://imgflip.com/i/45rmf2
... to grasp the concept that you don't need to know where files are so long as the OS knows.
This is not one step too far. It is a two-year backpacking trip across all of Asia too far.