The only real disadvantage is that the Y-harness represents another point of failure. There are two reasons why a 2 battery system is employed in a plane, more battery capacity and redundancy against failure. If you're going for redundency then you need to eliminate any point of failure that will knock out your entire battery system. This means that you need two batteries, two switches, and two separate connections into the receiver. While the chances of a Y-harness failing are slim, they do exist. If the batteries are connected into the receiver on two separate channels then no one component failing will knock out power to your receiver.

Hope this helps

Ken