The Creation Kit is a highly useful tool set for doing content mods like quests and locations. It makes it very easy to get into modding and work on a wide but shallow array of things, which is why the majority of modders wait for it (because most mods are going to have shallow bits and pieces even if they're very deep).

However, a mod as major and engine-tearing as Skyrim Together is going to have to work outside the bounds of the Creation Kit, and the Creation Kit is going to have a very minor impact if any on it, because it doesn't have those shallow bits and bobs. It isn't adding content, quests, locations, or anything like that. Skyrim Together is not modifying Skyrim, it's modifying the framework in which Skyrim exists (and Creation Kit is used to mod inside the world, largely).

It's perfectly reasonable to be working on a multiplayer mod this early. Heck, it's not impossible to be working on moving over many large mods because it's largely the same engine (let's be real, the 2 means nothing). It would probably be easier with the Creation Kit in some ways, but it's not a necessity for the more technically-advanced mods because those mods often work around the Creation Kit anyway.