This makes me want to pick Godel Escher Bach back up, anyone else?
It may well be the initial decision is subconscious and although we then (sometimes) inspect it in a meta/conscious way (and recursively if we are thinking hard), the article is saying we shouldn't confuse the meta process with the original thought. That original thought is derived in an unknown way. Its akin to the subsymbolic vs symbolic discussion elsewhere on HN in my opinion. The unconscious thought being the ANN (subsymbolic part) the meta function examining that thought and procesing it further being the symbolic part(consciousness).