For me as well, especially once I related it back to Parfit's Hitchhiker.

I have a physical definition of causation too. This is why I think CDT 1-boxes. Our universe is causal.

Our universe is also logical, as I'll explain in a bit. But, importantly, if you think CDT one-boxes then your 'physical definition of causation' is different from the definition of causation held by people who think CDT two-boxes.

Consider the twin prisoner dilemma. You and your psychological twin are put into rooms, have to choose whether to cooperate or defect, etc.; you might have the belief in a logical connection between your reasoning and your twin's reasoning (such that if your reasoning leads you to defect, theirs will as well, and if your reasoning leads you to cooperate, then theirs will as well), but you can't believe in a physical connection between your reasoning and your twin's reasoning (this particular voltage in your brain is in the causal history of that particular voltage in their brain). And so if you only reason based on the physical effects that you have on the universe, you end up defecting, because as much as you would like to signal your willingness to cooperate to your twin (and get a guarantee from them) you don't have the mechanism to do so.

If one has a logical definition of causation (as well as a physical one), then you reason as follows: two calculators, even if physically separated, will get the same answer if they run the same computation. What my decision is doing is working out how a particular computation terminates, so I can think as if I'm choosing both my action and my psychological twin's action, much like one calculator can expect other calculators will reach the same mathematical result. So reasoning "If I cooperate, then my twin will also cooperate" is valid for the same reasons that "if my calculator says 3*17 is 51, then other calculators will say the same." [Note that this is actually a different sort of validity than "if I place a ball in a bowl, it will stay there"--if I placed the ball on a hill instead, the ball would roll, but if my calculator miscalculated 3*17 as 37, that wouldn't change math--and that different sort of validity is why CDT doesn't respect it.]

If Omega is a perfect predictor, and you are presented the two boxes, well, the only possible answer is yes.

This is not how CDT reasons about its possible actions; it assumes that it can sever all connections to parent nodes whenever it makes a choice. So even in the 100% world, CDT using the causal graphs you provided and would two-box. This is actually a feature. [Thus, the way Omega maintains perfect predictive ability is you never seeing the full box.]

The correct action in transparent Newcomb's is to one-box when you see the money, even if Omega is only 99% accurate. [Depending on the formulation, it can also be right to one-box when you don't see the money, but it's cleaner to assume Omega's prediction only depends on what you do when you see the money.] Notice that your decision theory does better when it closes its eyes, which seems like a weird feature for a decision theory to have.

My entire understanding of FDT and how it varies from CDT or EDT is based on Eliezer and Nate's paper that I linked to, so I will only comment on what I think they mean. If someone was complaining that "Omega favors irrationality" and expanded that statement to "The choice they reward favors irrational persons", I would make the argument that rewarding people based on the choice/action they take is not an "unfair" scenario.

Some excerpts from FDT:

The standard defense of two-boxing is that Newcomb’s problem rewards irrationality. Indeed, it is always possible to construct dilemmas that reward bad decision theories. As an example, we can imagine a decision rule that says to pick the action that comes earliest in the alphabet (under some canonical encoding). In most dilemmas, this rule does poorly; but the rule fares well in scenarios where a reliable predictor rewards exactly the agents that follow this rule, and punishes everyone else. The causal decision theorist can argue that Newcomb’s problem is similarly constructed to reward EDT and FDT agents. [...] Newcomb’s predictor is not filling boxes according to how the agent arrives at a decision; she is only basing her action on a prediction of the decision itself. While it is appropriate to call dilemmas unfair when they directly reward or punish agents for their decision procedures, we deny that there is anything unfair about rewarding or punishing agents for predictions about their actions. It is one thing to argue that agents have no say in what decision procedure they implement, and quite another thing to argue that agents have no say in what action they output.

So that's the "cannon" take on "Omega favors irrationality".

On the second half of your comment:

I'd agree that you one-boxing would be evidence that Omega had given you the Million $. If you went through Newcomb's problem using "Of the actions I could take, which one would provide the most Bayesian evidence that I was going to get lots of utility?" you would one-box. However, that process is not the decision process specified by CDT. We're now talking about EDT (which as this comment [LW(p) · GW(p)] points out, is sorta wonky).

If that doesn't feel satisfactory, and it still feels like CDT would one-box, it might be useful to explicitly go through the exact decision process that you think CDT prescribes.

Here's a pretty good primer [LW · GW]