Recognising a bunch of high-frequency words is very much the foundation of reading.
Historically reading was taught by learning words with some very basic rules for pronunciation. It worked pretty well for a long time. But the pronunciation of non-trivial words - and some trivial words - has to be heard to be learned.
For example: it's not unusual for bookish people to mispronounce obscure words because they've never heard them. They know what the words mean, but the correct pronunciation just can't be worked out from the spelling.
The only way to learn it is to hear someone saying it.
Just because there are exceptions doesn't mean the rules are nonexistent. We're just rarely or never explicitly taught these rules.
Let's keep kids' achievement measures out of the cynical distrust of our teaching staff.
Edit: Yes, I am biased. And, TheOtherHobbes made better and clearer points than me in my sister comment.
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.