When the custom function is set to use both the internal and the external batteries (the default), the internal batteries will drain faster and when the internal batteries are drained, the flash will cease to work until they are replaced.
When only the external batteries are used to charge the flash, the internal batteries are used only to power the electronics of the flash but not to charge the flash so they will last longer. The disadvantage of using the external batteries only is that the cycle time is slightly longer than when both the internal and the external batteries are used.
So, if you need the fastest recycling time possible (at the expense of replacing the internal batteries more often), leave the custom function at the default (use both external and internal batteries). But if you want the internal batteries to last the longest between battery swaps, set the custom function to only use the external batteries.