The two battery systems are not connected. The motor is getting power from one and the receiver, servos, gyros and other electronics are being powered by another battery. These types of systems are using an Opto ESC that has no included BEC ( battery eliminator circuit ). The single battery method is using an ESC with a BEC in it to supply power to those other components as well as the motor.
Having the control electronics separated from the motor power means if the motor power is used up, you still have power going to the controls. The two potential down sides are the added weight and finding a place for the additional battery.