The True Sith were there from the very beginning of the Mandalorian Wars. They conducted everything so that the Jedi would be destroyed... according to Revan via HK-47. The Council believed the true threat... the True Sith... had never revealed themselves because they were afraid to face the Jedi directly. This indicates that the True Sith may not have been so great a power as some have made them out to be... I won't say names.
If the True Sith couldn't directly face the Jedi even after the Civil War, then it's not so outrageous to have the story start shortly after TSL. If there were ever a time that they would have attacked the Republic or Jedi, it was then. They would not have just decided to give them time to recover so that they could have a fair fight. The idea that they would wait 300 years after TSL is ridiculous.
The True Sith are the enemy behind everything in KOTOR and always have been. Naturally, they should be the enemy that is defeated at the end of the saga.