Because Boeing wired it that way
But seriously:
The APU on the -200 shuts down on the ground when the battery is shut off because you have lost APU fire DETECTION capability which comes from the Battery Bus. The Battery Bus is powered inflight by TR3.
Why you would turn off the battery in flight I am not sure but on e situation that comes to mind would be a suspected overcharging of the battery or a looming thermal runaway.