If you poke around on the Dryden site there is a similar project going on about autonomous refueling for UCAV's using probe & drogue. They need to work out the logic for how the UCAV would chase down the basket flexing around at the end of the hose

Seems maybe a bit silly since the US has the ability to refuel via flying boom. In that case the UCAV would just park itself behind big momma and get plugged in.

Anyway, I believe the autonomous nature in the original case also refers to the fact that you can't expect a pilot to hold a precise formation needed for efficiency for multiple hours and not get worn out. This kind of thing would need to be done by the autopilot as well.