In my view, the chief form of "dependence" that needs to be discriminated is inferential dependence and causal dependence. If earthquakes cause burglar alarms to go off, then we can infer an earthquake from a burglar alarm or infer a burglar alarm from an earthquake. Logical reasoning doesn't have the kind of directionality that causation does - or at least, classical logical reasoning does not - there's no preferred form between ~A->B, ~B->A, and A \/ B.

The link between the Platonic decision C and the physical decision D might be different from the link between the physical decision D and the physical observation F, but I don't know of anything in the current theory that calls for treating them differently. They're just directional causal links. On the other hand, if C mathematically implies a decision C-2 somewhere else, that's a logical implication that ought to symmetrically run backward to ~C-2 -> ~C, except of course that we're presumably controlling/evaluating C rather than C-2.

Thinking out loud here, the view is that your mathematical uncertainty ought to be in one place, and your physical uncertainty should be built on top of your mathematical uncertainty. The mathematical uncertainty is a logical graph with symmetric inferences, the physical uncertainty is a directed acyclic graph. To form controlling counterfactuals, you update the mathematical uncertainty, including any logical inferences that take place in mathland, and watch it propagate downward into the physical uncertainty. When you've already observed facts that physically depend on mathematical decisions you control but you haven't yet made and hence whose values you don't know, then those observations stay in the causal, directed, acyclic world; when the counterfactual gets evaluated, they get updated in the Pearl, directional way, not the logical, symmetrical inferential way.