“Then God said…” refers to a sequence of interventions by God of one sort or another, not necessarily creation ex nihilo. That is grammar being read correctly. The atmosphere becoming translucent and then transparent do not require acts of creation ex nihilo.
And I’m not sure about ex nihilo, anyway. I think it’s cool rhat quantum mechanics is hinting that the fundamental reality of the universe is information. That’s not nothing.
Again, that’s not necessarily nothing.