Despite some (already mentioned) shortcomings, I like it: it provides a simplified "real life" big picture of the whole process with sample tools; a thing that (in my experience) every other "getting started" guide seems to miss (most of them just mentions what is a makefile).
I also like the overall format of the website and the radio feature is a nice touch. I'll visit it again in the future, out of curiosity.
A follow-up article may extend it with collaboration (git) or may delve in either Unix-like (e.g. with the GNU utils etc) or Windows, or both. But the author should first address the highlighted shortcomings...
Common things are simply by category and subcategories starting from the media/file "type" (e.g. books, photos, etc).
Projects are created in a ~/playground directory and are eventually moved to a ~/projects one (but sometimes they just stay in a RAM-disk; i.e. experiments).
Within coding projects I usually have /src, /doc (by category and subcategories) and /utils (with utility scripts, Docker-related files, etc) sub-directories.
PDF et similia that don't fit within a specific project typically are generic enough to be placed somewhere under ~/books.
The main issue with this system is that there could be work-related things under distinct paths (e.g. ~/documents/work/<org> and ~/projects/<name>), but those may be archived together...