It doesn't mean that "the server isn't configured to parse %23 as # in a URL": it means that replacing # with %23 is precisely the method that must be used to access a file with a # in its name. So the server should absolutely not try to figure out it should be a simple anchor #.
An app replacing # with %23 is just as stupid as if it replaced slashes with the appropriate %-code, which would also break the URL's.