Ask yourself why you are running two packs. The two most common reasons are backup and current. A “Y” between battery and RX belongs in neither setup.

If using as a backup system, the "Y" represents a single point of failure which was mentioned. Not much point in running redundant batteries if you don't have redundant switches and paths all the way to the RX. A "Y" into the RX from batteries has no use if your goal is redundancy. There are better systems with fail on switches (or no switch) and load balancing systems that prevent failure from both opens and shorts in the system.

If using a second battery because your current loads are too high for a single pack, usnig the "Y" is self defeating because of the wire gauge and current rating of the pins. If in a high current situation, you should be using at least 18ga or larger wire from battery to RX which will be hard to pull of in a "Y", and the standard servo connector is only rated for 3A, which is probably well below what you are expecting to pull if you are putting in a 2nd battery for current reasons.