The Sherman act is a very simple act, and nothing in it say anything about the DOJ. Feel free to point out otherwise.
Maybe you want to try to argue the various Supreme Court decisions interpreting the Sherman act say something about the DOJ.
AFAIK, they don't.
The DOJ guidelines are simply used as guideposts for companies to understand how the DOJ is likely to view a proposed act.
That's it. The DOJ doesn't have to follow them.
It even says this in the guidelines:
"By stating their general policy, the Agencies hope to
assist those who need to predict whether the Agencies will
challenge a practice as anticompetitive. However, these
Guidelines cannot remove judgment and discretion in
antitrust law enforcement."
3. A finding about Amazon will be completely irrelevant to Apple's conduct in this case. The question is whether Apple committed horizontal price fixing. Amazon's possibly illegal conduct is going to be completely irrelevant in that, as horizontal price fixing is still per-se illegal. They could prove Amazon hurt the market a lot. They could prove whatever they like. As long as the DOJ proves they committed horizontal price fixing, it's game over.
Now, the supreme court may, in the end, decide horizontal price fixing should be analyzed under the rule of reason instead of being a per-se violation, but that's completely irrelevant to the current state of the law, and in fact, Apple's behavior. SCOTUS is not going to change the doctrine because they think Apple did the right thing here, they will change doctrine because they think the doctrine was wrong in general. However, that doctrine is the current state of the law, and what this case, and the appeal, will be analyzed under.
4. Bob Kohn is a guy who made his living off running companies dedicated to digital revenue for books. He has a huge stake in this game, and in fact, has unsuccessfully objected to every settlement that doesn't agree with his theories. You should be very wary of his legal viewpoint. It's like listening to Florian Mueller talk about Microsoft or Oracle. The only difference is that Bob Kohn has been rebuked directly no his theories by judges a large number of times now, whereas Florian has just been wrong without having the pleasure of Judges directly address his craziness.