A paper is not a generic facility for data storage. Text meant for human reading is to some degree sequential. You cannot just change the order of words, paragraphs or sections in it. It would be a different text. But that doesn't mean files in a directory should have inherent order.

Also, they say: "Note that we are not condemning hierarchy in general; indeed, hierarchy can be useful in a variety of situations. Rather, we are arguing against canonizing any particular hierarchy"