Good work finding some real world examples that are at least similar to the hypothetical.
But in those cases, the military aircraft was the only one involved in the crash, and in the first case, it came down on a Federal reservation, and there’s no indication that the FAA or NTSB even wanted to become involved.
In jnglmassiv’s hypothetical, the military aircraft collides with a civilian aircraft, and the FAA and NTSB want to collect the debris as part of their investigation of the crash. In that scenario, I don’t think that the military can actually block FAA and NTSB investigators from the crash site or from collecting debris.
As I wrote, though, the most likely realistic result of that hypothetical is that the DoD coordinates with the FAA and NTSB, and at worst a bureaucratic squabble gets resolved at the Cabinet level.