Sorry, doesn’t make any sense at all to me…
Once you connect the 2 batteries in parallel, you basically have one battery with twice as many cells. It would seem to me that if you hooked up two 12 volt power leads, you would be charging at 24 volts to a 12 volt system.
So, the only explanation I can think of is that particular charger has a switcher built in that alternates the power on and off to each bank of the charger. Therefore, the charger is still charging 2 batteries with one bank of the charger at any given time.
If you hooked up 2 separate 12 volt chargers to those batteries while they are connected in series, you would either fry your charger immediately or blow the battery when the charger is plugged in. I know this from experience.