The Amtrak Charter was for "intercity passenger" service, replacing that service that was provided by the railroads previously. The point of intercity and commuter operations is for transportation and getting folks from Points A-Z. Commuter railroads also were there for local transportation, not intercity service like ATK. Over time, ATK did operate some commuter operations as a contracted operator. (Caltrain, Metrolink)
The Silverton, although still having passenger rates as controlled by the CO PUC, had not been in the business of transporting folks from Durango to Silverton and return as a means of transportation for many years. By that time ATK was created, it was primarily an excursion operation for the enjoyment of the scenery and history.
I would think that ATK would have had nothing to do with the Silverton operation, only the DRGW intercity train (RGZ)
MDR