But a couple of difficulties arise. The first is that if TDT variants can logically separate from each other (i.e. can prove that their decisions aren't linked) then they won't co-operate with each other in Prisoner's Dilemma. We could end up with a bunch of CliqueBots that only co-operate with their exact clones, which is not ideal.

I think this is avoidable. Let's say that there are two TDT programs called Alice and Bob, which are exactly identical except that Alice's source code contains a comment identifying it as Alice, whereas Bob's source code contains a comment identifying it as Bob. Each of them can read their own source code. Suppose that in problem 1, Omega reveals that the source code it used to run the simulation was Alice. Alice has to one-box. But Bob faces a different situation than Alice does, because he can find a difference between his own source code and the one Omega simulated, whereas Alice could not. So Bob can two-box without effecting what Alice would do.

However, if Alice and Bob play the prisoner's dilemma against each other, the situation is much closer to symmetric. Alice faces a player identical to itself except with the "Alice" comment replaced with "Bob", and Bob faces a player identical to itself except with the "Bob" comment replaced with "Alice". Hopefully, their algorithm would compress this information down to "The other player is identical to me, but has a comment difference in its source code", at which point each player would be in an identical situation.