From their perspective, they don't need to consider it.
The CDT agent can have a credence of 0 in the proposition that they will get $M + $1000. After all, if they have a credence of 1 that the predictor is perfect and a credence of 1 that they were a two-boxing sort of agent at t=0 then they should have a credence of 0 that they will get $M + $1000. The CDT agent won't deny this.
They then say, however, that they have a credence of 1 in the world state where there is $0 in the second box. Given this credence, the smart decision is to two-box (and get $1000) rather than 1-box (and get $0).
So the short answer is: they don't even consider this possibility but this doesn't change the fact that, on their view, the best decision is to two-box.
I'm not entirely sure what we're discussing here but what I'm saying is that the view isn't internally inconsistent: they don't have contradictory credences in world states and they don't think that there is an option of two-boxing and getting $M and $1000 (they assign credence 0 to this possibility - of course, presuming they have credence 1 that they were a two-boxing type of agent at t=0 then they also assign credence 0 to the possibility of one-boxing and getting $M because they hold that what matters is the decision type at t=0 and not the decision at t=1).
So if you're saying that their view is internally inconsistent in one of the above ways then one or the other of us is confused. On the other hand, if you're just saying that this way of thinking seems alien to you then what I've said in this comment is pretty much irrelevant...
They then say, however, that they have a credence of 1 in the world state where there is $0 in the second box. Given this credence, the smart decision is to two-box (and get $1000) rather than 1-box (and get $0).
Ah, right, they never expect anything to be in the opaque box, so for them taking the opaque box is basically redundant ("might as well, no harm can come from it"). So they correctly assign the probability of zero to the event "I'm a two-boxer and there is $1M to be had".
However, this is supplemented by "CDTer must two-...
With much help from crazy88, I'm still developing my Decision Theory FAQ. Here's the current section on Decision Theory and "Winning". I feel pretty uncertain about it, so I'm posting it here for feedback. (In the FAQ, CDT and EDT and TDT and Newcomblike problems have already been explained.)