Hi, Watabou!
First of all, I would like to express all my respect for your work and I'd like to clarify that my intent is not to criticize it, but it is to make myself available for any help.
I agree with you when you say to "let users interpret a map as they like". Indeed, my suggest was about adding an "option" to give the opportunity to use another interesting tool to the City Generator (which doesn't exist yet or, perhaps, I haven't found it yet). Infact, not all the cities are flat as London, Paris and Barcellona (e.g. see in UK Dover Castle, Edimburg Castle, Beeston and Peckforton castles, in France Carcassonne or Haut-Koenigsbourg, in Spain Casteldefels, etc.). If you see at Italy or east-europe cities, you will see wonderful medieval mountain cities with their fortifications on cliffs, mountains or hills. Castles can be on the sea, inside the city, near to the walls and on mountains (these are generally the locations to control enemies or citizens and protect the city or the power).
I simply saw that your (already wonderful) generator has a lack about orography, so I reported it to you.
I hope I was helpful :)