Here is a link confirming what I said above:

http://www.battle.net/scc/faq/other.shtml

Why are Locations square, rather than isometric like the tiles?
The isometric look of StarCraft is achieved in StarEdit by combining square tiles that have isometric image characteristics. For performance and technical reasons, StarCraft maintains terrain internally on a rectangular grid.
The Location Properties dialog can be used to make a location apply only to certain elevations, thereby making it conform to the shape of terrain underneath it.