This could simply be mischief with an off-the shelf, gasoline, quad copter with upgraded long range radios. Flashing green strobe would be an FAA navigation light -- if viewed from the other side you would see a flashing red.
All of the natsec and domestic spying theories would be nullified by the thing having nav lights.
Also entirely possible they used some stock parts and just didn't realize the LED was there.
I only think an amateur would make that kind of mistake. If it was from a hostile power with any kind of competence, I think they would have extensively tested it in simulated operational conditions. If they didn't notice the light when they initially built it, they would have probably noticed it during testing.
This would be beneficial for a two person team. The drone operator watching the video feed and a spotter providing positions of pursuit aircraft.