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Finally got around to looking at this. I didn't read the paper carefully, so I may have missed something, but I could not find anything that makes me more at ease with this conclusion.
Ben has already shown that it is perfectly possible that Y causes X. If this is somehow less likely that X causes Y, this is exactly what needs to be made precise. If faithfulness is the assumption that makes this work, then we need to show that faithfulness is a reasonable assumption in this example. It seems that this work has not been done?
If we can find the precise and reasonable assumptions that exclude that Y causes X, that would be super interesting.
For example, in theorem 3.2 in Causation, Prediction, and Search, we have a result that says that faithfulness holds with probability 1 if we have a linear model with coefficients drawn randomly from distributions with positive densities.
It is not clear to me why we should expect faithfulness to hold in a situation like this, where Z is constructed from other variables with a particular purpose in mind.
Consider the graph Y<-X->Z. If I set Y:=X and Z:=X, we have that X⊥Y|Z, violating faithfulness. How are you sure that you don't violate faithfulness by constructing Z?
I'm not quite convinced by this response. Would it be possible to formalize "set of probability distributions in which Y causes X is a null set, i.e. it has measure zero."?
It is true that if the graph was (Y->X, X->Z, Y->Z), then we would violate faithfulness. There are results that show that under some assumptions, faithfulness is only violated with probability 0. But those assumptions do not seem to hold in this example.