Because the way the certification was agreed was the aircraft would achieve a full civil certification and then a military delta would be applied. This was supposed to be quicker than doing a full military clearance as Airbus had experience of dealing with EASA.
However, I know from personal experience, that it was almost getting to the stage in the avionics and human factors certification panels that the delta was getting so large, it would be easier to go for a military certification and then certify the civil delta.
Regards