1. Restored scene completely absent in retail where Kreia returns to Malachor and shows Sion which one of them has the real power, explaining why he is subservient to her when the Exile encounters him later
2. Your core party members (Atton, Visas, Mira, Mical/Brianna), separated from the Exile on Malachor, launch an attack upon Kreia and Sion and are easily beaten- it's up to the exile to save them or let them die- Atton in particular gets a nice melodramatic death scene (way too much overacting by his voice actor)
3. There's an actual resolution to the Remote/G0-T0 standoff involving HK-47, according to your actions in the HK-Factory, which determine the fate of Malachor V.
I mean, Malachor isn't finished by any stretch of the imagination, but the modders obviously squeezed everything they could out of what was present in the voice files.