The article did not clearly explain what cognitive science has to do with phonics, which AFAIT is a heuristic system for Western languages. So when I studied Chinese as a child, how did I learn to write Chinese, nonphonetically, without confusing horses and ponies? A heuristic is an optimization but not fundamental but the article clearly asserts that phonics is fundamental to language in that if you don't use phonics you get illiterate students... I think there's some conceptual conflation or some middle case being ignored by the author: A) Is [formal instruction in] phonics necessary? v.s. B) Is 3-Cue harmful? These are not proper opposites.
Here's a provocative claim made in a more sciencey article I just found:
"The linguist David Crystal (2003) estimates that the phonics can explain only about 50 percent of English spellings."
And further down:
"As the linguists Venezky (1967) and Carol Chomsky (1970) explained, English prioritizes the consistent spelling of morphemes over the consistent spellings of phonemes."