I really don't think you need to do it at the vert. If you are going to use the colour map then use the colours there and screw the verts. It would work just as well.
The idea about the booleans would probably work just as well. You could then layout the city just as you want. https://www.schloerb.com/tutorial/greeblecity_1.htm that might help as far as doing the city layout goes.
Just thinking this would be a cool mel tutorial to do. I may have a crack at this myself 

Alan
Technical Director - Framestore
Currently working on: Your Highness
IMDB