Presentation of Newcomb's problem in section 11.1.1. seems faulty. What if the human flips a coin to determine whether to one-box or two-box? (or any suitable source of entropy that is beyond the predictive powers of the super-intelligence.) What happens then?

If the FAQ left this out then it is indeed faulty. It should either specify that if Omega predicts the human will use that kind of entropy then it gets a "Fuck you" (gets nothing in the big box, or worse) or, at best, that Omega awards that kind of randomization with a proportional payoff (ie. If behavior is determined by a fair coin then the big box contains half the money.)

This is a fairly typical (even "Frequent") question so needs to be included in the problem specification. But it can just be considered a minor technical detail.