Ignoring the B744 case where the APU battery powers a stand-by DC bus,
AFAIK one of the primary drivers of a separate APU battery is so that a cold soaked, hard starting APU won't almost stuff your ships battery. Think about it - would you really want to launch at night in dodgy weather with a ships battery(s) strongly charging after being flogged by an APU start? Think also of the air start case with, say, B767 - what about an aborted start off the ships battery, now badly flogged? 30 minutes anyone?
It's just too easy and simple to have a dedicated APU battery and ease the regulatory burden by leaving the ships battery alone in case of major electrical failure necessitating APU start in the air. Don't tell the bean counters, but it's also good engineering practice to segregate systems whenever possible.