The 4th hole is for look pedals. Their cleats have a piece in the centre that bolts into that hole and stays on the shoe. When you replace the cleat the piece remains on the shoe and acts as a guide for the new cleat so that you do not have to worry about the position of the new cleat. I wish Shimano SPD-SL cleats had the same feature.
As for running SPD cleats there is an adaptor that Shimano makes just for this application. Part# SM-SH85
