If you want a place only the server can get to, why don't you make an offset into some wall or something and put a shield or something in there. Make the way in really complicated and blocked completely by the 3rd layer.

I don't think Trigger Zones and stuff will work, though. Perhaps you could create the area blocked by walls, have a trigger crate or zone undo that, and once you get inside of the place have a trigger zone that reblocks the entryway. But according to what JelZe said, you may have to complete all of that before anyone else joins or something. Who knows. Why do want a secret area, anyway?