The big problem with this process is that the civil authorities will not certify an aircraft system that has redundant capability ie a more demanding military role, so following civil certification a lot of systems will be ripped out and replaced with the military kit and the process begun again.
Huh? Civilian certification is about flight testing to establish that an aircraft has performance that meets or exceeds minimum performance requirements decreed by civilian authorities. If an aircraft exceeds those performance requirements, then it will be certified. Having "redundant" capability is irrelevant.
Please clarify your argument.