The 3dskyboxes are in the map they're used in. They're just at 1/16th scale and seperate from the rest of the map. have a look around in the .vmf, you'll find it quickly. Obviously the guide itself must be outdated. Or Valve are lazy.
You basically make a miniature world, surround it with the Skybox entity/ texture, and stick a camera thingy in the middle, look at cbble.vmf for a better idea.
Open up... whats it called, the Mansion one... in CS:S and go looking around in Spectator, that one has a really nice skybox to give you a good idea of how to do them.