Ignoring the story reason, the point of the barren lands in the gameplay is so later in the game you can refresh and make the land lush or purple so you can settle somewhere in the late game, if you so desire. Also, it can be used to set up outposts and such to create a battle ground so civilization cities are not always next to each other. There are some spells that you can only cast in neutral territory and as such you need a good place to put neutral territory that makes sense.
Also, the way they determine what land is settable is by a series of numbers associated with a tile, a barren tile does not get as many bonuses and as such will lower the possibility of settling and also provide poor spots to settle when near barren landscape.
The last thing is to provide variety in the landscape beyond just green grass and purple death land. Provides a better artistic feel and makes the landscape feel more realistic.