I think Neal Stephenson was overly optimistic about the audience for this book, and I think he would regard it as a failure of the book that the only people reading it are people like us who can make the distinction you just made. He seemed to be writing for people who knew nothing that he hadn't already told them, and identifying CLIs with Unix was a simplification that I think was supposed to make it easier for his target audience to follow.

I did give the book to my computer-phobic father to read, because he was a historian who was interested in social and cultural changes and also kind of curious about what I did for a living, and he said it was interesting, but he also said he didn't really understand it at a concrete level and was relying on the vivid metaphors to get any meaning out of it. I don't think he really considered it worthwhile for someone like him to read, which I think meant it was a fundamentally ill-conceived book. Still a fun read, though.