The isogonal contours are complex shapes influenced by continents, oceans and the earth's core.
Have a look at this to see what I mean:
http://www.geomag.bgs.ac.uk/images/c...pdf/merc_d.pdf
As I understand it, a GC track is defined as the intersection of a plane that passes through two points on the surface plus the earth's centre, and the earth's surface. This may differ minutely from the shortest distance definition, but is practically identical.