There are tons of reason why there might be a 3 am departure.
First off....do you live near an airport?
It could be an aerial survey, could be a freighter, could be training.

What do you define low as. The general public has huge problems determing the real altitude of aircraft.

FedEx doesn't directly fly prop aircraft but they do employee sub-contractors that do.

As far as seeing the N number at night.....good luck. Its not like that number is lit up.