Remeber that, taditionally, enemies of the United States were not afforded constitutional protections. It would be absurd to try to grant due process rights to an enemy onthe battlefield, and until recently we've had the sense not to try.
Remeber further that Article III deals with treason (which is essentially when an American attacks the U.S.). Congress has power to decide how treason is punished. It is fully constitutional and proper for treason to be punished differently than ordinary crime.
Bona fide terrorists are enemies of the U.S. They fall into one of the two catagories above, depending on their citizenship. In either case is it innapropriate for them to receive the same rights we want honest men to receive.
So long as the P.A. is applied exclusively to bona fide terorists, there are no constitutional or moral problems. Again, the only real problem is that there are no assurances that only terorists will receive this treatment.