So just like any other system, starting with the UNIX system interface, the various shells, the autotools and everything else. Stuff is built on top of other stuff and it is impossible to fully predict the future and start out with a clean design that anticipates all future needs.
Granted, that is, I agree.-
PS. What the article means by "mess" (in context) is the article's entire gist, that is: "Things have evolved, but they have done so in a way that is ..."
... wrong, counteranimical to the web's "original purpose", opposed to user-interests, etc., etc., ...
... however one would want to define all those things.-
Personally, I think the description the author makes of then vs now, has merit.-