The argument being made is not ‘org-mode is a reasonable alternative to a filesystem for organizing textual files’, it is ‘org-mode is a reasonable lightweight textual markup language’.

The fact you can replace entire project and documentation systems with org-mode is not an argument in favor of its lightweight text markup.

Yet text markup doesn't exist in a vacuum, heavy or light. Text is marked up in the first place so it can be better processed by a computer, while keeping it reasonably readable by humans. And there are a variety of markup formats out there as some given person gets the idea that doing it X way makes it most ideal for both use cases. Org-mode is a extremely lightweight, likely more so than md, AND allows for complex levels of processing WHILE maintaining that lightweightedness. The feature variety already exist as proof, at least in Emacs.