Your quite right! I just tried it with my Bowens Esprit set up. The ST-E2 does not sync the Bowens with the 580EX, resulting in an image in which the Bowens isn't recorded. Yet the 580EX in manual mode mounted on the camera syncs perfectly. I don't know why I thought it worked before. Sorry for confusing you. It explains why I had bought the Pulsar wireless trigger!
Right, the ST-E2 still fires the pre-flash even when the remote 580EX is on manual mode. If you set up an optical slave flash, it will trip before the shutter is open. Irksome.
If you mount the 580 EX directly on the camera and set it to manual, there is no pre-flash and it syncs with optical slaves.