Update:
The exporters for CityEngine 2015.2 do include atlas generation functionality.
Texture Settings: Create Texture Atlas
Creates texture atlases which combine a set of textures into one, thus reducing the number of textures and materials.
All textures except COLORMAPs are removed.
Note: in case of repetition (i.e. uv coordinates outside [0,1]), textures can not be put into an atlas.