How much different are civilian and military aircraft autopilots?
There is no civillian autopilot for an F-16, because there are no non-military F-16s. Ditto with the F-117 or or B-1 or B-2, so who knows what unique modes those autopilots have for their uniquely military missions (i.e. dropping bombs or low level terrain following). However, when the military aircraft has a non-military equivalent (KC-10/DC-10, KC-135/B707, C-40/T-43/B737, C-21/Learjet, T-44/C-12/KingAir, etc) then the autopilots are generally identical.

Any differences are more likely to be found in FMC software rather than in the Autopilot, and those differences would be very specific to each aircraft &amp; its mission.