I find the reasoning specious. In particular, files and programs are the same in MS-DOS and Unix. You can, for instance, ls the ls command or cat the cat command. He's also completely ignoring the superiority of the file system's namespacing (by directory) to just having two global buckets like in elisp.

The execute bit comparison is especially specious. If I try to execute a non-executable file, it fails. It doesn't go look for an executable file with the same name. Same as if I try to invoke 0 in Clojure. e.g. (0)

He's right that the symbol resolution of the first entry has different rules but ignores the fact that the shell isn't very good at higher order commands. Which is probably okay for a shell but not much use for a modern programming language.

Finally, he's right that multiple namespaces are a good idea, but that's Accepted Truth these days. It's just that we think namespacing should be under the control of the dev, not dependent on the type of the variable.