The Thompson Center Firestorm, RMC Accura and the Traditions PA Pellet can shoot sub powders, even in pellet form, so they claim. I have talked to people that own them and the do claim that the rifles will shoot sub powders. BUT they also claim they had some ignition problems from time to time. All of that is solved with a duplex of black powder first, or going to pure black powder. BUT I agree.. if its a flintlock, shoot black powder and your problems will be solved.
My Thompson Center Black Mountain Magnum is a traditional style rifle but I am not sure they were made in flintlock. But the Black Mountain Magnum can shoot pellets. It is because of a different style fire channel. The Black Mountain Magnum has the same fire channel as the Firestorm.