RTF is a global modification that replaces all towns in the game.

Okay, but how do you set up a unit icon so that it can be seen as a unit icon in the map editor?

Take a look at how it's done with the Psatki units; the icons are stored separately from the mod in the complet/icon folder, and the link to this icon is provided in the file located in the MapObject/_(AdvMapObjectLink) folder.