It also doesn't seem reasonable to think that the operators of the craft decided to come all the way to Earth just to expose some random humans to their exhaust fumes, and then casually drift off over some trees. These factors don't mean the object wasn't alien. It just means there isn't sufficient reason to think it was.
Something I wonder about is how burning (jet) fuel/flames, could cause radiation burns? If the craft was nuclear powered, would it still produce flames? (I know nothing about nuclear propulsion.)
It seems odd to me that the craft would have both chemical and nuclear propulsion systems.
The assumption that there was a nuclear aspect to the craft comes from the symptoms experienced by the witnesses, right? Would burning fuel/flames cause similar symptoms? I don't believe so.
For what it's worth, whether human or non-human, I don't believe the craft/pilots intended to buzz the car/witnesses, but that's just my opinion.
If this was a (non-human) UFO in distress, that might explain the mundane performance (and the 20+ helicopters shadowing it).
One other detail I've wondered about is what other phenomena might cause the symptoms the witnesses had. Although I haven't watched the witness interviews (blush) I did catch on the Paracast that the one woman was acting coy about where they had been... Did they get themselves into some kind of trouble; had they done something or had they been somewhere they shouldn't have been? It's well documented that people sometimes create wild stories to hide certain truths sometimes...
Of course theres the unsubstantiated issue of the road being torn up. Wish this could be proven conclusively. It would really go a long way toward backing up the witnesses testimony.
As far as this craft being a military prototype: my limited understanding is that military prototypes are regularly declassified over time. Has there ever been a craft resembling the one in this case which has been declassified?
Also, my unqualified opinion is that it would be absurd for the military to test a prototype, nuclear powered flying craft in a populated (albeit sparsely) area, one that required the assistance of 20+ helicopters. (Is there any precedence for that in military literature?)
This seems like a craft that would be better tested in the desert.