In any case, the issue in the linked article seems to be a classic case of Goodhart's Law: "When a measure becomes a target, it ceases to be a good measure".
Which is to say, phonics is very important, and a great tool in a balanced approach to learning to read for fun and profit... However, it's not so great to focus on phonics as a lonely and narrow target in a national reading programme, or to justify Departmental failures.