I agree with this analysis. The most interesting case is a third variation, in which there is no evil Omega, but the organic genetic lesion causes not only a preference for smoking but also weakness in resisting that preference, propensity for rationalizing yourself into smoking, etc. We can assume happens in such a way that "Susan actively chooses to smoke" is still new positive evidence to a third-party observer that Susan has the lesion, over and above the previous evidence provided by knowledge about Susan's preferences (and conscious reasonings, etc) before she actively makes the choice. I think in this case Susan should treat the case as a Newcomb problem and choose not to smoke, but it is less intuitive without an Omega calling the shots.
In that case she should still smoke. There's no causal arrow going from "choosing to smoke" to "getting cancer".
I stumbled upon this paper by Andy Egan and thought that its main result should be shared. We have the Newcomb problem as counterexample to CDT, but that can be dismissed as being speculative or science-fictiony. In this paper, Andy Egan constructs a smoking lesion counterexample to CDT, and makes the fascinating claim that one can construct counterexamples to CDT by starting from any counterexample to EDT and modifying it systematically.
The "smoking lesion" counterexample to EDT goes like this:
EDT implies that she should not smoke (since the likely outcome in a world where she doesn't smoke is better than the likely outcome in a world where she does). CDT correctly allows her to smoke: she shouldn't care about the information revealed by her preferences.
But we can modify this problem to become a counterexample to CDT, as follows:
Here EDT correctly tells her not to smoke. CDT refuses to use her possible decision as evidence that she has the gene and tells her to smoke. But this makes her very likely to get cancer, as she is very likely to have the gene given that she smokes.
The idea behind this new example is that EDT runs into paradoxes whenever there is a common cause (G) of both some action (S) and some undesirable consequence (C). We then take that problem and modify it so that there is a common cause G of both some action (S) and of a causal relationship between that action and the undesirable consequence (S→C). This is then often a paradox of CDT.
It isn't perfect match - for instance if the gene G were common, then CDT would say not to smoke in the modified smoker's lesion. But it still seems that most EDT paradoxes can be adapted to become paradoxes of CDT.