If I understand the suggestion to be that turning the switch to "off" would leave the battery or batteries out of the charging loop, I agree that you should not do that, ever, while the motor is running. Even if the battery is dead and won't take and hold a charge it nevertheless provides a voltage sink for alternator output. Running an unloaded alternator will frequently cause them to fail. Don't know exactly what it is you are hoping to accomplish by running the vehicle while "off", or if that was even your intention, but don't do it.
The size of the alternator, i.e. 130A versus 60A, has very little to do with whether it will "charge" two batteries. You can charge two batteries in tandem with a 2A charger, and I do it all the time, so having 60A or more on tap is hardly a problem. Your charging system is not intended to bring batteries from dead to full charge no matter how many amps you make or how many batteries you have. You should only be using 10 to 15A tapering down from there to maintenance amperage, and I would expect any alternator to be able to do that for two batteries as well as one, even if it takes a few more minutes to do it.
If what you want to do is support a winch, the larger alternator is your friend, but not because of the number of batteries you have. Rather, it tends to fill the gap on electrical demand for short periods of time, so a larger alternator will provide more current for a few moments longer during times of high demand, and will take a few minutes less to recover batteries after discharging during winching. If you winch a lot, buy a larger alternator. If you don't winch very often, don't worry about it.
