they just say that it doesn't matter if the predictor is perfect or not as, given that the boxes are already filled, it is too late to influence the thing which would lead you to get the $M (your agent type at t=0 rather than your decision at t=1).
That's where they lose me. By definition of a perfect predictor, there is no option of "two-box and get $1000 and $1,000,000" in the problem setup, why would they even consider it?
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...
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.)