Probably because there's no elegant way to support all the potential edge cases of that default behavior. For instance, if you introduced a reference with that format, you can't refer to it later - if you use the static number and it changes, you're now pointing to the wrong reference. So it reduces to using names, and the hassle of coming up with a name for each new link or footnote reduces to just using numbers - so the only thing that needs to be supported is manually named or numbered items.
The author correctly describes the ideal solution - a plugin that replaces unnamed links before saving or such - but likely fails to understand why that (as opposed to adding behavioral cruft to a markup language) is the correct level of abstraction for such a solution. Imagine if a project like wikipedia was riddled with the ambiguity of dozens of people's various attempts to wrangle the autonumbering to their writing.