Yeah I figured it was shell customization gone awry early on, with 'mkdir --' in the mix. But if they'd figured that out immediately it wouldn't have been a fun post; busting out some custom unix plumbing tools and showing how cool they are is really what the article is about. Also gotta admit they have a pretty darn fun github.
That would've been writing a custom kernel extension to track this down, but fortunately tracing exists these days.
Seriously, I don't see anything wrong here, it's about the same route I would've gone down. Except the other way round because writing a custom ~/bin/mkdir would've saved me reading up.