SCv2 can easily be connected to the controller terminals, and it is best to do so, because it will minimize the amount of current flowing through the cables.
The motor, when supplied with power from any other power source, will draw less current from the battery.
SoC calculations would then depend on where current is sensed. If it were just one battery, it'd be defined by that battery's BMS. With a Power Tank, maybe it's less clear, but I would hope the current sensors are relative to the battery and not to the controller or motor.
I think the only problem is to run the generator so that it could operate in a stable way despite a variable load or a shifting load (mostly the load is the motor, until there's regen and then it's the battery, and then it'd have to transition to idle without lurching). Or, basically what I said above.