I am hoping someone can just explain it rather than saying that it simply "is."
The agency model is what keeps the price of apps on the app store low. Developers (agents) can charge whatever they want, but clearly that doesn't equate to automatic sales at whatever price. It is in fact a very competitive market.
Nothing about the agency model, as I see it, in the example of the App Store has even a hint of being anti-competitive.
How is this different for books? I just don't see it. But I am open to explanations.
If anything is anti-competitive, it is selling at a loss so that nobody else can enter the market. That is what Amazon was doing.
Price fixing requires collusion between the producers to all sell at the same price point. It's certainly possible this is going on with the big publishers in Apple's store, but that doesn't require Apple's participation in the collusion. It doesn't exonerate Apple either, it's orthogonal.
In the wholesale model that traditional booksellers and Amazon use, it's still possible for publishers to price fix. It's possible for book sellers to price fix.
It seems to me that Agency vs Wholesale doesn't really have much to do with the concept for price fixing.
What am I missing?