This is an interesting question. It was actually the redundancy of the CS menu that made me decide to re-purpose it for The Trapdoor (re-play modes in the form of CSs, version 1.3 onwards). I'm glad I didn't know how to hide it at the time, otherwise I wouldn't have had the idea. It would be good to know, though.
Edit: this is where is go on about my theory, which turned out to be totally wrong. See below.
The other possibility is that the launcher does something snazzy, like somehow patching the exe in memory. If that was the case, you wouldn't be able to do it in a mod unless you had really good knowledge of the engine and you made your own special launcher. I'm guessing that if any of us were that good at programming engines then we wouldn't be here!