The in game minimap is nothing more than a BLP file generated by the editor when you save. The editor looks at features like terrain, destructables, doodads, cliffs, ramps etc and renders them to the image. If these features change during the game, eg a tree is chopped down, then the minimap image is not updated to reflect this. Features such as units and camera view are rendered on top of the minimap image by the game.
One can import a custom mimimap BLP file to overwrite the one automatically generated by the editor. This can show different features, be an artistic interpretation of the map or anything one wants. In game managed features will still be rendered on top of it though, which may or may not be desirable.