If we're worried about lost opportunities for short-lived animals, are we also worried about lost opportunities for counterfactual animals that easily could have existed?

Yes, it would be hard give a good reason for treating these differently, unless you're a preference utilitarian and think there is no point in creating new preference-bundles just in order to satisfy them later. I was arguing from within a classical utilitarian perspective, even though I don't share this view (I'm leaning towards negative utilitarianism), in order to make the point that suffering dominates in nature. I see though, you might be right about factory farms being much worse on average. Some of the footage certainly is, even though the worst instance of suffering I've ever watched was an elephant being eaten by lions.