Well, probably because the initial cause of the fire could well be a battery problem even if the batteries themself are unarmed. For example, if they produced to much power it's possible that the wiring became overheated and at a specific point (a weak point where there's for example flamable material arround the wiring) caused an actual fire. Before such a fire happens it can easily take a while even hours. While there may not be any damage to the batteries they may be the root cause.
So in the end, they cause of the fire could well be the batteries. Which I don't say is the actual cause, this is something the investigation will tell us eventually but because the fire happened somewhere (far) away from the batteries it's not something you can easily rule out.
Well no, not really. Batteries do not 'produce' power in that sense, they supply it. If battery power is available to a faulty circuit then, yes, damage could result as they will supply the energy needed to cause the problem but the 'cause' is still the fault in the circuit, not because of any fault in the battery.
My memory is that the 787 APU batteries are isolated unless they are needed for an APU start and I'm not sure the APU power wires would be routed where the damage is visible anyway.