I do wonder how they're going to get round this provision: either the FAA will have to retract the offending paragraph or Boeing will have to use a different type of battery. I suppose the third way will be to argue "we don't know what caused it but we've changed lots of things so it's OK now"; depends on how much spine the regulator has that morning, I suppose...
Or perhaps a compromise could be reached for the FAA to say OK so you have done some substantial changes to the battery and given that if it should fail the box will prevent it from setting fire to the aircraft, we will give you a CofA but with a temporary restriction of 180mins ETOPS only, (ie the same as for a non functioning APU.) if after 12 months there have been no more incidents then we will lift this restriction. They could also demand that any batteries swapped out and returned to the manufactures are opened in the presence of an inspector from the Japanese regulators.