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
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The civilian certification requirements are MINIMUM standards required. If a manufacturer wishes to install systems that have BETTER performance then there would be no objection from the certifying authorities. In your example the oxygen system would be superior to civilian certification standards, so there would be no certification issues at all.
I still don't understand why the need to meet civilian certification standards is a problem.