Welcome to the forums and thank you for your interest in Simutrans-Extended.
At present, there is no feature that allows height maps to encode where cities may be stored. If you would like to play on a height map with cities in realistic locations, you will need to generate the map without cities and then switch to the public player mode (CTRL + P) to add them manually. Do not forget to switch back to the default player to play the game when you have finished.
