This is a common area of concern, Farsight. It all depends on the artist.

There are some of us that rely heavily on tectonic action and Earth geology to make our maps (myself included). But for the fantastic ones, they start with that base map and use "magic" to explain certain ground-breaking instances (i.e. deity battles) to explain certain regions.

There are times when you can get extremely creative and use magic as the sole reason. There is an interesting discussion about this in here.
http://www.cartographersguild.com/sh...pinion-Welcome