I have noticed that the compasses on my boat are not properly calibrated. That is the mechanical compass, the fluxgate compass on the Furuno, and the fluxgate compass on the Simrad never give the same bearing. They are out by at least 10 degrees. This raises the question of which fluxgate compass will govern when a waypoint is set.
When it comes to Autopilot navigation (including waypoints) your Simrad compass will be the only one coming into play. Also in terms of comparing mechanical to fluxgate, make sure you are looking at both units without variation included. Furthermore, each compass will experience deviation differently since they should be located at different places in the boat.