CPU voltage is different. That can vary based on how much load is placed on the processor. On those, the Auto setting will add extra (possibly unnecessary) voltage to maintain stability.
Speeds of QPI and HyperTransport and other system links won't change during use if set to Auto. The bad thing is that you don't know what the board will choose for the setting. If you want to keep it near a certain speed, you have to set it manually.