If there are multiple translations, then either the translations are all mathematically equivalent, in the sense that they agree on the output for every combination of inputs, or the problem is underspecified. (This seems like it ought to be the definition for the word underspecified. It's also worth noting that all game-theory problems are underspecified in this sense, since they contain an opponent you know little about.)
Now, if two world programs were mathematically equivalent but a decision theory gave them different answers, then that would be a serious problem with the decision theory. And this does, in fact, happen with some decision theories; in particular, it happens to theories that work by trying to decompose the world program into parts, when those parts are related in a way that the decision theory doesn't know how to handle. If you treat the world-program as an opaque object, though, then all mathematically equivalent formulations of it should give the same answer.
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...
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.