The reason I think it all matters is the argument is that Apple and the publishers were artificially inflating prices. By looking at Amazon's pattern of behavior, I think it's at least highly arguable they were artificially deflating prices.
Remember, every publisher set their "retail" prices for the eBooks, which was above the $9.99 Amazon was discounting to. They were setting the prices separately. If there was a true market going on when Apple entered the market, there would be stores that did no discounts, stores that deeply discounted a few books but not all, stores that deeply discounted all of them.
But due to Amazon's anti-competitive behavior, there was a market of one, and they made sure that market remained a market of one by discounting to the wholesale price (and threatening publishers who objected with removing their physical books from Amazon as well as eBooks).
So I'll go back to say if the DoJ had both said "the most favored nation clause won't fly in this market, it's anti-competitive" and had taken Amazon to task to stop their anticompetitive behavior, that would have led to a more open and competitive market, where retailers can enter and compete. By only going after Apple, they aren't creating an open market, they're creating an even less free market.