[...] assume that the universe and its initial conditions can be described succinctly and inferred by A, and that the sequence of bits sent over W1 and W2 can be defined using an additional 10000 bits once a description of the universe is in hand.

Do you mean, "once a full description of the universe is in hand", and that the 10000 bits are the complexity of locating W1 and W2 in the full description?

• A's outputs are fed to the output wire W2, the rest of the universe (including A itself) behaves according to physical law, and A is given the values from input wire W1 as its input. (Model 1)
• A's outputs are ignored, the rest of the universe behaves according to physical law, and A is given the values from W1 as its input. (Model 2)

Model 2 still has to locate W1. What might be the complexity of locating W2 conditional on having located W1? It seems plausible that this extra complexity would be within a constant of the complexity of describing the AIXI algorithm and something like counterfactual physical reasoning about alternative inputs, to check whether the known behavior of AIXI is consistent with W2 given counterfactual input at W1.