I think you're misunderstanding something, but I can't quite pin down what it is. For clarity, here is my analysis of the events in the thought experiment in chronological order:
1. Omega decides to host a Newcomb's problem, and chooses an agent (Agent A) to participate in it.
2. Omega scans Agent A and simulates their consciousness (call the simulation Agent B), placing it in a "fake" Newcomb's problem situation (e.g. Omega has made no prediction about Agent B, but says that it has in the simulation in order to get a result)
3. Agent B makes its decision, an...
Yes, perhaps that sentence wasn't the best way to convey my point. This version of CDT does not in any way acknowledge backward-causality or subjunctive dependence; the idea is that since the predictor runs a simulation of the agent before deciding on its prediction, there is a forward causal influence on the predictor's action in the case that the agent is a simulation.
Thank you so much, this is exactly what I was looking for. It's reassuring to know I'm not crazy and other people have thought of this before.