What happens when two different voltages are connected to a car battery
When the SmartPass conducts to allow current from the alternator to flow directly into the house battery bank, it shorts out the Smart Charger disabling it. This is similar to placing a copper wire right between the input and output of the Smart Charger. This forces the Smart charger to basically turn off. Note this is different from a short-circuit where you connect the output of a power source straight to ground. This is a short across a device which electrically removes the device from the circuit. 

Put another way, electrons take the easiest possible path. If you provide an alternate path that takes practically zero effort to traverse, practically all electrons will take that path and practically no electrons will take the other paths leaving the devices in those paths without power to operate.

So in your scenario at least, you are not actually connecting different two voltage sources together (unless you consider the output of a functioning battery charger or alternator being connected to a battery to be that which it is. But you already know what happens there. The larger voltage wins and shoves current into the devices with lower voltage)