I assume (please correct me if I'm mistaken) that you're referring to the payout-value as the output of the world program. In that case, a P-style program and a P1-style program can certainly give different outputs for some hypothetical outputs of S (for the given inputs). However, both programs's payout-outputs will be the same for whatever turns out to be the actual output of S (for the given inputs).
P and P1 have the same causal structure. And they have the same output with regard to (whatever is) the actual output of S (for the given inputs). But P and P1 differ counterfactually as to what the payout-output would be if the output of S (for the given inputs) were different than whatever it actually is.
So I guess you could say that what's unspecified are the counterfactual consequences of a hypothetical decision, given the (fully specified) physical structure of the scenario. But figuring out the counterfactual consequences of a decision is the main thing that the decision theory itself is supposed to do for us; that's what the whole Newcomb/Prisoner controversy boils down to. So I think it's the solution that's underspecified here, not the problem itself. We need a theory that takes the physical structure of the scenario as input, and generates counterfactual consequences (of hypothetical decisions) as outputs.
PS: To make P and P1 fully comparable, drop the "E*1e9" terms in P, so that both programs model the conventional transparent-boxes problem without an extraneous pi-preference payout.
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): ..."...
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.