I'm not sure I agree that the matrix sections work. They do look nice, but that means that some of the actors end up trying to compete with them. But again they make no real sense. I'll accept that a mind in control of the matrix is forced to impose some kind of order upon it (though this point is made in The Deadly Assassin and not in TToatL), and you could interpret the unmasking of Popplewick simply as the Doctor managing to focus his mental energy on revealing the controlling intelligence - except we already know the Valeyard is the controlling intelligence so... and then attempts at logic sort of break down. I've never really understood the point of the matrix bits, I think the Valeyard wants the Doctor to sign away his lives, and then kill the Doctor but he's not going about it terribly efficiently - The Deadly Assassin was much clearer and more focused about how the logic of the matrix parts is working and how they contribute to the Master's plans. And its all mixed up with this last minute plot to kill everyone in the courtroom. It seems as much of a mess as the rest of the story to be honest, to many ideas, not enough thought about how they all fit together.

Voyager is great though.