Metaphor? Not quite. A symbol, yes, but symbols can be an actual, physical occurence. Turning to a non-LDS source, the late Martin Buber (On the Bible, p. 53), there is the following observation on the meaning of signs in the Bible. "It is a symbolization, a sensory presentation of a manifested truth, a perceptible reality which, no matter whether it is more or less "wondrous," always reminds people once again of that truth." Same goes for baptism, and, indeed, the cleansing power of the atonement. As Buber goes on to say, "What is now only existent in words will then take on real existence."