If your plan is to run the water through your Berkey anyway, I wouldn't worry about the safety of the water (these are food grade water barrels, I assume, right?). Yes, the water may pick up the taste of plastic or certain gasses can diffuse through the plastic when stored for very long periods, but that's a palatbility issue.

Actually, I suppose that palatibility can also be a real problem. When you (or maybe your family, like children) are stressed and overworked during/after some disaster, "funny" tasting water can lead to drinking less than what you need and lead to dehydration, possibly heat injuries, or at least unnecessary fatigue.

Besides the aeration idea, keeping powder drink mixes handy is another idea.