Yeah, that's right - so I think the proponent of CDT can be criticised for all sorts of reasons but I don't think they're (straight-forwardly) inconsistent.
As a note, the decision in NP is whether to take the opaque and the transparent box or whether to just take the opaque box - so the CDT agent doesn't just think they "may as well" two-box, they think they're actively better to do so because doing so will gain them the $1000 in the transparent box.
And yes, I agree that considerations of free will are relevant to NP. People have all sorts of opinions about what conclusion we should draw from these considerations and how important they are.
OK, thanks for clearing this CDT self-consistency stuff up for me.
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.)