A typical Civil cert nonsense is having to install a civil crew Oxygen system that is only designed to keep the crew alive whilst they carry out an emergency descent to a safe altitude. Whereas the military system would keep them alive whilst flying straight and level depressurised at 40K ft plus as required by the aircraft specification.
If you had a cargo hold full of paras/passengers and had a pressurisation problem at altitude the military Oxygen system would still allow the emergency descent as its a more capable system
EASA insisted that for civil cert of the A400M only a 'civilian' Oxygen system was allowed on the aircraft. Other military equipment/systems were required removed by EASA as the 'covered or inhibited during civil cert testing' option was not an option.
So rather than a civil certification falling off the back of a military one we waste money testing an aircraft no one has bought - a civilian cargo aircraft.