CDT acts to physically cause nice things to happen. CDT can't physically cause the contents of the boxes to change, and fails to recognize the non-physical dependence of the box contents on its decision, which is a result of the logical dependence between CDT and Omega's CDT simulation. Since CDT believes its decision can't affect the contents of the boxes, it takes both in order to get any money that's there. Taking both boxes is in fact the correct course of action for the problem CDT thinks its facing, in which a guy may have randomly decided to leave some money around for them. CDT doesn't think that it will always get the $1 million; it is capable of representing a background probability that Omega did or didn't do something. It just can't factor out a part of that uncertainty, the part that's the same as its uncertainty about what it will do, into a causal relation link that points from the present to the past (or from a timeless platonic computation node to both the present and the CDT sim in the past, as TDT does).

Or from a different light, people who talked about causal decision theories historically were pretty vague, but basically said that causality was that thing by which you can influence the future but not the past or events outside your light cone, so when we build more formal versions of CDT, we make sure that's how it reasons and we keep that sense of the word causality.