The problem, as I see it, is the wording in 5.1 is not clear enough and has lead NZF to falsely believe Article 6 is valid for Wynne's case.
Instead of saying 'permanent nationality' it would be better to say 'primary' or 'first' nationality. ie the nationality you are entitled to when you're born.
Altering this wording makes it so much clearer that Article 6 is only referring to those players whose original nationality could entitle them to play for more than one country (eg US passport for Guam), and that Wynne's case clearly falls into Article 7.