It was a customer requirement that a number of the 787's systems be able to be operated without the engines or APU running or the plane having to be connected to external power.
Why Boeing didn't employ two discharge limits - one for ground operations and one for emergencies in the air - is due to it adding complexity to the fault tree and the necessity to take into account the possibility that the ground discharge limit activates during an emergency, denying the flight crew power and possibly directly leading to an accident.
The as-designed system works when operated as-designed. Ground crew need either better training as to how long they can operate the plane off just the battery and/or better supervision to ensure those limits are not exceeded.