"the Raspberry is actually powered from the USB output of the controller" I don't know about his controller but these cheap controllers will power the USBs eve

"the Raspberry is actually powered from the USB output of the controller" I don't know about his controller but these cheap controllers will power the USBs even on low battery. They will kill the battery (he even mentions this bellow). The right way to have USB output is to connect a car charger to the 12V output of the controller and then connect your load to that charger. That 12V output is cut when the battery is low and reconnected after it is charged. These voltages can be set in the controller. This way the battery will never discharge so much that the controller doesn't even recognize the type of battery (6V, 12V)