This conversation is a bit confused. Looking back, P and P1 aren't the same at all; P1 corresponds to the case where Omega never asks you for any decision at all! If S must be equal to S1 and S1 is part of the world program, then S must be part of the world program, too, not chosen by the player. If choosing an S such that S!=S1 is allowed, then it corresponds to the case where Omega simulates someone else (not specified).
The root of the confusion seems to be that Wei Dai wrote "def P(i): ...", when he should have written "def P(S): ...", since S is what the player gets to control. I'm not sure where making i a parameter to P came from, since the English description of the problem had i as part of the world-program, not a parameter to it.
According to Ingredients of Timeless Decision Theory, when you set up a factored causal graph for TDT, "You treat your choice as determining the result of the logical computation, and hence all instantiations of that computation, and all instantiations of other computations dependent on that logical computation", where "the logical computation" refers to the TDT-prescribed argmax computation (call it C) that takes all your observations of the world (from which you can construct the factored causal graph) as input, and outputs an action in the present situation.
I asked Eliezer to clarify what it means for another logical computation D to be either the same as C, or "dependent on" C, for purposes of the TDT algorithm. Eliezer answered:
I replied as follows (which Eliezer suggested I post here).
If that's what TDT means by the logical dependency between Platonic computations, then TDT may have a serious flaw.
Consider the following version of the transparent-boxes scenario. The predictor has an infallible simulator D that predicts whether I one-box here [EDIT: if I see $1M]. The predictor also has a module E that computes whether the ith digit of pi is zero, for some ridiculously large value of i that the predictor randomly selects. I'll be told the value of i, but the best I can do is assign an a priori probability of .1 that the specified digit is zero.