The backward link isn't causal. It's a logical/Platonic-dependency link, which is indeed how TDT handles counterfactuals (i.e., how it handles the propagation of "surgical alterations" to the decision node C).
My understanding of the link in question, is that the logical value of the digit of pi causes Omega to take the physical action of putting the money in the box.
See Eliezer's second approach:
2) Treat differently mathematical knowledge that we learn by genuinely mathematical reasoning and by physical observation. In this case we know (D xor E) not by mathematical reasoning, but by physically observing a box whose state we believe to be correlated with D xor E. This may justify constructing a causal DAG with a node descending from D and E, so a counterfactual setting of D won't affect the setting of E.
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.