the problem with charging both batteries at once is that most chargers are peak chargers now a days. Once one battery peaks it's going to shut off the charger, whether the other is peaked or not.
no 2 batteries are going to charge the same, and charging them separately also lets you diagnose charging issues
For instance, I had one battery die in my 1600, the other was taking up the slack. If I had just charged them in parallel I probably would have never diagnosed that one battery was no good.