You've read the term "base layout" in articles explaining how to make an efficient base, but this article refers to a different meaning of "layout".
When a map is loaded, you usually already have a human and alien base. The data describing what buildings are where is called a "layout". It is possible for server owners to create additional layouts for maps. So, they could move bases to different places, or they could add the missing medistation in Tremor or build both bases under the map's basement etc.