The first difference between civil and military testing is that the military service is both the customer and the approval authority. In the civil arena, the operator is the customer and the FAA/EASA/??? are the approving authority.
However, the major difference is that with the military service as the approving authority, they have to pay for any changes. I once worked on the FAA certification of a military transport. This "off-the-shelf" approach was intended to reduce the cost of flight test. However, there were some relatively minor changes (mostly dealing the NVG compatible cockpit lighting) mandated by the FAA which had to then be changed when the airplane went into service.
By the way, most FAA flight tests are flown by company or consulting designated engineering representative pilots, not by FAA employees.
Goldfish85