The person who creates a terrain also creates the clipboard map. They can choose the color palette, terrain topography details, detailed grid lines, etc. They can also add, as has been stated, supply lines (roads/tracks) to each base/strat. It's not dynamic; it's a static image that can be created in Photoshop. The game overlays the actual bases, strats, radar, etc. on top of the static graphic that is the clipboard map.
The big problem with marking the supply lines, as has also been mentioned, is if objects get moved those markings no longer mean anything.