Manafort’s attys are claiming that these indictments did not emerge from any investigation re collusion. They were old matters from USAs in Virginia 12 years ago. The only reason they are being used today is to force anti Trump testimony from Manafort. The judge wants to see the DoJ order creating the SC because while it might say he can investigate other matters stemming from collusion, it does not say he can seek out other matters from the past, not associated in any way with collusion, and use them as a club to make Manafort a cooperating witness.
This is like a lawyer representing a suspect who was arrested for stealing a car in New York City ... and he's trying to get the charges dismissed because the arrest took place in the 20th Precinct and the arresting officer was assigned to the 30th Precinct.
Manafort's lawyers seem to be making a political argument here, not a legal one.