My previous aircraft had a blue mountain EFIS system in it. This had it's own GPS map built in as well. This unit used an external magnometer (electronic compass) which had to be precisley aligned with the fore and aft axis of the aircraft but this was so that the primary flight display could show aircraft heading just as you would see on a compass. The GPS page still displayed track over the ground. I now have a Garmin 296 installed in my RV6 which does not have an external magnometer so it will only know track over the ground.
Interestling in my RV6 I have a vertical compass card which to be honest are not that accurate and a real pain to try and set up. On occasion when I have mentioned this to some people they have mentioned why don't I just align the DI with the GPS, so although I think it's quite obvious what the difference is between the GPS and the compass there are plenty of people who don't. Even when I explain it, it sometimes takes a while for the penny to drop. Not that these people are stupid in any way, they just hadn't quite thought about it enough.
I know some will say that this is why GPS is bad and can contribute to airspace busts but come on all modern GPS are moving maps and if air space is shown on your right then turn left a little untill you avoid it. I quite often let friends have a little go and show them on the GPS map any airspace near us and they are quite capable of steering the plane away without any knowledge of track, headings etc.
Just a shame I can't fit the new garmin 695 in my panel