This variation of the problem was invented in the follow-up post (I think it was called "Sneaky strategies for TDT" or something like that:

Omega tells you that earlier he flipped a coin. If the coin came down heads, it simulated a CDT agent facing this problem. If the coin came down tails, it simulated a TDT agent facing this problem. In either case, if the simulated agent one-boxed, there is $1000000 in Box-B; if it two-boxed Box-B is empty. In this case TDT still one-boxes (50% chance of $1000000 dominates a 100% chance of $1000), and CDT still two-boxes (because that's what CDT does). In this case, even though both agents have an equal chance of being simulated, CDT out-performs TDT (average payoffs of 500500 vs. 500000) - CDT takes advantage of TDT's prudence and TDT suffers for CDT's lack of it. Notice also that TDT cannot do better by behaving like CDT (both would get payoffs of 1000). This shows that the class of problems we're concerned with is not so much "fair" vs. "unfair", but more like "those problem on which the best I can do is not necessarily the best anyone can do". We can call it "fairness" if we want, but it's not like Omega is discriminating against TDT in this case.