Our B&G Hydra Pilot really works well in apparent wind. It's other functions aren't that much different from other quality autopilots.
When motoring we will usually use "NEMA" (i.e., waypoints of the GPS) if we have layed in a course. Otherwise its "Compass".
Occasionally, when sailing, we'll use NEMA (or, rairly, compass) if we're concerned with a navigation hazzard or feature -- but then only if we're pretty confident that wind won't shift.
I think that if you sail a lot, it would be a mistake not have the apparent wind function and use it -- as long as you have the instrument system with that as a feature.