Geoid vs Ellipsoidal

Are there any sources of altitude which use a geoid-based datum present in Mission Planner or arducopter software? I am planning waypoints and using a GPS (3dr ublox) which output elevations based on a WGS84 datum, but I am seeing an elevation bias between my planned waypoints and the AGL values from LIDAR (Lightware SF11/C) after a flight which seem to correspond to the difference in geoid and ellipsoid elevation in my area.