For problem 1, in the language of the blackmail posts, because the tactic omega uses to fill box 2,

TDT-sim.box1,box2=(<F,T> <T,T>) -> Omega.box2=(1M, 0)

depends on TDT-sim's decision, because Omega has already decided, and because Omega didn't make its decision known, a TDT agent presented with this problem is at an epistemic disadvantage relative to Omega: TDT can't react to Omega's actual decision, because it won't know Omega's actual decision until it knows it's own actual decision, at which point TDT can't further react. This epistemic disadvantage doesn't need to be enforced temporally; even if TDT knows Omega's source code, if TDT has limited simulation resources, it might not practically be able to compute Omega's actual decision any way but via Omega's dependence on TDT's decision.

any other agent who is not running TDT ... will be able to re-construct the chain of logic and reason that the simulation one-boxed and so box B contains the $1 million

There aren't other ways for an agent to be at an epistemic disadvantage relative to Omega in this problem than by being TDT? Could you construct an agent which was itself disadvantaged relative to TDT?