The first shellfish and corals evolved to survive in the CO2 levels that existed AT THE TIME THEY AROSE. The extinction occurred during a time of quickly changing acid levels that the organisms could not adapt to quickly enough: like the one we're undergoing now (unless some mechanism kicks in to turn it around).

For that matter, the first marine life must have evolved when there was no free oxygen in the atmosphere at all, CO2 levels were through the roof and sea water acidity was very high. And note the spike in CO2 levels on that chart right around the time of the extinction event in the article. That is consistent with the article's conclusions.

The general trend of CO2 levels since the Permian extinction event has been down. The trend over the last 60 years (the data coverage I linked to), has been climbing.

Incidentally, CO2 dissolves in water to form a weak acid, it doesn't kill things outright, but it interferes with the formation of carbonates for shells. It doesn't have to kill everything, just interrupt the food chain to provoke an extinction. The excess carbon is removed from the water by limestone (CaCO3) formation. But calcium carbonate also dissolves in water, so an equilibrium is eventually reached. A sudden surge or shortage of CO2 can provoke change in the water's pH. This is what they think is killing the coral now.

I'm only speculating, but I would bet that big dip in CO2 levels starting around -450Myr is due to the colonization of the land by plants. Multicellular life arose over half a billion years ago, about the time that CO2 curve was peaking, I'd wager.