The entrances to Exadian cities are sealed with permeable force fields. They keep the dangerous surface environment out and the vital interior atmosphere inside. Without them the planet wouldn't be able to support any of its native sapient life. 

However there are a number of species that have been able to survive on the surface. Eventually some of them could evolve into sapient forms and there would essentially be two entirely different worlds in one. Not that there isn't different biomes on this planet already, It's just the division would be more pronounced.