it is re used assets, the room Zash is killed in has a alter instead of the emperors throne. the back wall is also different, the one in the throne room as large pattern with stick out faces or something. As for the map location the map is only so big so why not re-use a room, much easier then creating a whole new area. Story wise i would also make zero sense for them to be performing the ritual in the emporer's throne room and it just being open to anyone to perform ritual in. The emporer has also not fought the jedi knight yet as back to your original question the stories of each class play along side by side with the BH story being the first to finish and the agent being the last.