I believe one of the arguments used in the suit was along the lines of "Apple, by making the minimum price (other than 'free') for apps and IAPs 99c, prevents us from charging, say, 37c and this harms consumers and is anticompetitive". I believe it was just to provide a clear, verifiable argument that customers were being charged more than they would be in a free market (whereas other things Apple does are infinitely more serious, but also harder to prove and quantify). I'd guess the agreement addresses that to be consistent, even though I don't think anybody truly cares about the granularity of the price tiers.