You can alter those maps in BCT. You can add things like roads, elevated points, forest, etc. However, as Maddog stated you can't add brand new maps.
I should point out BCT, and I think ATF maps are not direct copies of orginal maps. It just represents the general area. There are enough maps in BCT to cover all kinds of terrain. Ex: You can take the Cuba map and use it for let's say Falkland Islands. It would be difficult to tell the difference.