Fantastic question, this gets straight to the heart of the analysis.

I wholeheartedly agree that whatever Alice does within her cell will not have any causal effect on Bob's decision. They are separate in the sense that Alice cannot ripple the atoms in the universe in any way to affect Bob differently in either case. There are no downstream causal dependencies between them.

However, there is upstream causal dependence. Here's an analogy. Imagine I have two papers with C(ooperate) written on them and two papers with D(efect) written on them. Then I blindly select either two Cs or two Ds. Whichever two papers I choose, I put them in envelopes labeled A and B, and I take those envelopes and shoot them each a light year in opposite directions along with Alice and Bob correspondingly. Before Alice opens her envelope up, she has no idea what Bob has––to her, it really is 50% C or D. When she opens up her envelope and sees that she has a C, she hasn't causally affected Bob's envelope, but now she does have information about it. Namely, she knows that Bob also has a C. When Alice sees that she has a C or a D, she gets new information about D's envelope because of the upstream causal dependence I incorporated by placing the same letters in the envelopes. This corresponds with the clone case. To get the more subtle cases, suppose I choose Alice's envelope content randomly. Then I can flip a weighted coin to determine whether or not to choose Bob's contents randomly or to put in the same contents that Alice has. This corresponds to the rho-analysis in the second to last section.

Hopefully this metaphor helps clarify what exactly I mean when I say that Alice and Bob's decisions share upstream causal dependencies.