Emerald is part of Compiz-Fusion, not a separate entity. Compiz manages the actual placement and movement of the windows, and Emerald handles the window decorations. Emerald doesn't replace Compiz, in fact I am fairly sure Emerald can't even function without Compiz running.
That said, you should be able to do transparent title bars with just gtk-window-decorator; I am looking at them right now. But Emerald does give you much more control over themes and such.