It's just another map.
It really isn't. There are considerable differences between bases and regular maps.
When connecting to a regular map, whether it's an open zone or an instanced mission (there is very little difference between the two), the server just sends a filename. Say, maps/City_Zones/City_01_01/City_01_01.txt. That's Atlas Park.
The client sees that filename and opens the appropriate geobin, inside of which are a bunch of GroupDefs and Refs that, handwaving away some complexity with the object library, tells the client how to build the geometry for the zone. The server has its own copy that it loads, and -- assuming the two of them are identical -- both client and server have an independent copy of the geometry and the player can move around without the client and server desyncing.
Base maps on the other hand branch off very early in the scene negotiation protocol. Instead of a filename, they send a compressed binary representation of the base itself. That format is completely different than the on-disk format for regular maps. Instead of groupdefs and refs, it contains high-level information about room layout, color schemes, base items that have been placed, even the contents of storage bins (ever wondered why the base would flicker and redraw itself when putting stuff in storage?).
When the client receives that information, it uses it to construct an in-memory map out of predefined groupdefs that contain pieces of rooms. There's a special base details file for base items as well that gets referenced. It's assumed that the server does the same thing in order to build up its representation of the scene; this is necessary to have the geometry in order to run physics and collision detection, which in COH is done serverside. This has to happen in exactly the same way on the client and the server for things to sync up; otherwise you get rubber banding.
With some dirty debugger tricks, it's actually possible to convince the client to write out the temporary map it constructed for the base in geobin (groupdef) format. That gives valuable clues about how the world is constructed from the base map and what needs to be done to replicate that process.