Re: military aircraft ...
"I assume that radar doesn't track those heights? Or is all tracking at that height transponders anyway?"
Air route surveillance radars are 2D, just show azimuth and range. The beam is shaped to be near the horizon, but if the target is far enough away it will be visible at ten miles up. The question is its speed; if it's way out of the doppler filter it would get rejected. Presumably somebody at the FAA is investigating to crosscheck vs. beacon data.