Traya was the de facto leader and master of both Sion and Nihilus, they both bent to her will, she was recognised as leader by the forces on Malachor V and the remaining Sith Lords out there, due to her being the former master of Darth Revan, this is made absolutely clear in the KotOR CG, she IS the leading Dark Lord of the Triumvirate.
This is not really true. The group was called the Sith Triumvirate. A triumvirate is a government co-ruled by three heads of state. Each three of these had there own powerbases, agendas, and schemes. In fact, a Kaggath could be held between the members of this triumvirate. Traya was not "in direct control". The others cooperated with her and her plans, but as seen with their betrayal, they obviously were able to resist her command. Notice that its a betrayal, not a mutiny. Therefor Traya should only have her powerbase, or the forces of Malachor V.