The logic behind it is that since the NG has no emergency source of electrical power (RAT) the APU is kept running so that in the event of a loss of a single or double source of electrical power, it can be selected on as quickly as the checklist requires without the worry that a cold soaked APU may not start when required.
The fuel burn (+/_ 300lbs/hr) is accounted for from departure to ETOPS Exit Point.