I think I've realised why NZF are looking at Article 6.
It's because the Cook Islands are a member of FIFA
This comment seems to have been overlooked from a few pages back.
Assuming you read article 5 as Wynne's permanent nationality (NZ) is not reliant on residence (living continuously in NZ), article 6 would be the applicable article based on the above, right?
Wynne's permanent nationality for FIFA purposes is SA, not NZ.
If that was the case, sections 6 and 7 would be redundant. Permanent nationality is the one acquired at birth.