On the other hand, if the main battery runs down that far, there is nothing to control. With more than one battery there is a good chance that the least noticed one, probably the RX one, will not be charged. Hopefully it will just leave the boat drifting, but it could leave an uncontrolled boat doing its own thing maybe flat out. Or, depending on wiring and ESC, reverse only.
Anyway, a separate BEC, if required, takes up less space and weighs less than almost any RX battery and will always give the proper regulated voltage as long as the main battery has enough go to drive the rest of the boat.
Of course, for a big collection of extras like lights, sounds, working goodies, a separate battery for them makes lots of sense.