GitHub renders markdown files. So the difference between clicking on navigation links in a documentation website and clicking on markdown files in a GitHub docs folder is... the CSS theme.
As I see it, the author of TFA is simply offering some heuristics for judging whether or not he's going to have a hard or an easy time working with a project's documentation. So in this view, presenting documentation using a structure that is specifically intended for documentation is taken as an indicator of care and attention to detail. I wouldn't say that he's arguing that a directory full of files isn't functionally equivalent or isn't useful.
(Personally, out here in the real world, I'll put up with all sorts of limitations — even a complete lack of documentation — if somebody else's existing code solves a problem that I have.)
(Personally, out here in the real world, I'll put up with all sorts of limitations — even a complete lack of documentation — if somebody else's existing code solves a problem that I have.)