I found this out rather by accident when I was replacing a dead start battery. I noticed voltage on the start battery leads after they were disconnected. That was odd, I thought since the charger had been turned off. I got verification from Mastervolt that the circuit doesn't care where it gets power, it feeds the start battery! The power source was my house bank. A worst case scenario could have ended up with both banks dead. Not a great design. The solution I chose was to isolate the banks using diode boxes supplied by Mastervolt. There's a jumper to adjust charger output voltage to compensate for the loss in the diodes. There are other solutions, but Mastervolt gave me a great deal on the diodes. Since your charger has only one output, you wouldn't have this gotcha. The combiner solution takes care of isolation issues.