I think pijul is a counterexample to this claim. Category theory was used to find the mathematically optimal semantic (i.e. interface) for the category of files

I think pijul is a counterexample to this claim. Category theory was used to find the mathematically optimal semantic (i.e. interface) for the category of files and patches (i.e. version control) and so the need to plan the command line interface has been minimized. A GUI would still require a substantial amount of work. I wouldn't go so far as to defend the somewhat exaggerated claim in the original article but I still think CLIs are easier than GUIs.