You might be interested in Cheating Death in Damascus, particularly section 3.1, which deals with CDT's instability, and which points towards a more satisfying version of counterfactual reasoning.

People argue about the Newcomb's paradox because they implicitly bury the freedom of choice of both the agent and the predictor in various unstated assumptions. Counterfactual approach is a prime example of it. For a free-will-free treatment of Newcomb's and other decision theory puzzles, see my old post [LW · GW].

Really well written and thought out.

Indeed, if both Alice and Omega know that Alice's decision-making will tell her to use the 1-boxer strategy, then Alice will know she will gain $1M

and

In both cases, her counterfactual optimization urged her to be a 2-boxer

feel like the crux to me.

If Alice was such a person to listen to the counterfactual optimization, then both Alice and Omega would not know she would 1box. There is a contradiction being buried in there.