Why on earth did Allison and Treize run after the train and not capture the dude delaying Treize? I'm sure they could have got something out of him with a little punching.

Anyway, I think the target might still be the princess. Just the prison dude concocted a really twisted and indirect plot of getting her. Maybe he didn't trust in their chances of succeeding in assassinating her while she was properly guarded on her own train, and so he calculated it so that she would be coming along with Travas to rescue Treize and Lillia. When that happens, it would be the prison dude's playground this time. Quite a risk to take, in any case.