That they actually got good legal advice is a speculation, and even if it were true they could have decided to ignore it thinking their strategy was worth the risk. Anyway the publishers settled almost immediately, most likely because their legal advice did not find the laws so ambiguous and the risk of an adverse judgement too high. Apple most likely simply had much more to lose.
The monopoly was not illegally obtained nor illegaly abused, at least until a judge says otherwise. Being a new entrant doesn't mean you can break the law to get a share of the pie, it's obvious you have to make investments which might be costly. Microsoft entered the gaming consoles market with 0% market share and managed to get a good share of the market after years of due investments. Apple wanted to do the same but without the due investment part.
The publishers wanted higher ebooks prices because they wanted to protect their declinig physical books market. They have zero interests in incentiving ebooks sales because in a world dominated by ebooks they become irrelevant: in the digital world you simply don't need them anymore and can publish directly through Amazon/Apple/whatever.
It's not speculation that apple had legal advice, some of the lawyers involved were called to testify. Apple seems to have a lot of lawyers, maybe they ignore them, who knows. On the other hand, are you speculating that Apple knowingly broke the antitrust law because it thought it "was worth the risk", or do you have some evidence to that effect?
That the publisher's settled says nothing about Apple's legal position. Apple played a different role in the deal. The publishers settlement with DOJ is a business decision, it simply shows that an admission of guilt and a fine was less expensive than the cost of defending themselves. Apple has publicly stated that they don't believe they did anything wrong and choose defend themselves rather than admitting to guilty. Some people may choose to believe that they are lying, but Apple has a history of putting their money where their mouth is when it comes to being a socially responsible company, that earns them the benefit of the doubt with me.
Amazon's obtained their 90% share of the e-book by being the first on the scene with a good e-reader, eBook store, and content delivery system; they earned that 90%. But e-books were not a "free market" where competition sets a fair price and drives innovation. I'm a capitalist at heart; I just happen to think that free markets are better.
The deals that Apple cut with the publishers don't seem unfair to me; publishers set the price for their product, pay Apple a share for the sale, and let Apple sell for as good a price as anybody else. Apple didn't dictate how the publishers made deals with anybody else. And Amazon wound up getting the same deal. It seems far more likely that another business could profitably enter into the e-book market following Apple's deal than before, so the market would be more likely to see competition. What Apple did with their deals was to eliminated Amazon's barrier to competition, a barrier Amazon held in place by selling popular e-Books at a loss.
Your example about Microsoft and X-Box is good, and Apple has frequently done the same thin. They win some, they loose some, it's how business works. But as long as Amazon was selling e-books at a loss, I don't see how Apple or anybody else could enter the market and expect to eventually make a profit on e-books. Do you have some profitable business plan in mind?
Your comment on why "The publishers wanted higher ebooks prices" is speculation. My suggestion that higher e-book prices would be an incentive for publishers to bringing more of their catalog to the e-book market is also speculation, but is the sort of things successful business do, they increase supply when there is a demand.
But may main point was that I think we have a problem in the US with antitrust laws. The laws should be clear, and I don't think they are (although I admit I am not a lawyer). I think there should be a compelling reason for the government to intercede in the free market, and in this case I don't see one. I don't see how DOJ's action promotes free and fair competition in the market.