Originally Posted by omens
I think I was under the assumption that Batman fixed the autopilot himself, though we don't get to see much ingenuity going on in the trilogy.
It was implied that he fixed the software bug, to enable the auto pilot function of the Bat.
In TDK, he did modify the original protype given by Fox of the transmitter-receiver in cell phones to generate pulse to map the surroundings and to spy on the City.
He also encrypted it with a null key encryption, showing that he could do some software programming.