So you're saying that if Omega predicts from your thought process, you choose one-boxing or not smoking, but if Omega predicts directly from the lesion, you choose two-boxing or smoking?
I don't see how that is relevant. The description I gave above still applies. If you choose one-boxing / not smoking, it turns out that you get the million and didn't have the lesion. If you choose two-boxing / smoking, it turns out that you don't get the million, and you had the lesion. This is true whether you followed the rule you suggest or any other. So if TDT recommends smoking when Omega predicts from the lesion, then TDT gives the wrong answer in that case.
If you choose one-boxing / not smoking, it turns out that you get the million and didn't have the lesion. If you choose two-boxing / smoking, it turns out that you don't get the million, and you had the lesion.
Well as I said above, this ignores causality. Of course if you ignore causality, you'll get the EDT answers.
And if you define the right answer as the EDT answer, then whenever it differs from another decision theory you'll think the other theory gets the wrong answer.
None of this is particularly interesting, and I already made these points above.
You're given the option to torture everyone in the universe, or inflict a dust speck on everyone in the universe. Either you are the only one in the universe, or there are 3^^^3 perfect copies of you (far enough apart that you will never meet.) In the latter case, all copies of you are chosen, and all make the same choice. (Edit: if they choose specks, each person gets one dust speck. This was not meant to be ambiguous.)
As it happens, a perfect and truthful predictor has declared that you will choose torture iff you are alone.
What do you do?
How does your answer change if the predictor made the copies of you conditional on their prediction?
How does your answer change if, in addition to that, you're told you are the original?