You use metaphors as scaffolding while you build your picture of the truth, step by step, always leaving something out. But I don't agree with you that we're using metaphors to express what is not metaphorical. All our attempts to understand deep truths are in some sense metaphorical. Math tells us one kind of truth. Images tell us another.
Most scientists go back and forth between the two.
There's a great story Viki once told me about two great physicists walking on the beach. One is explaining the mathematical structure of empty space. Of course, there is a danger in stepping too far away from the mathematics, as you suggest. The poet, too, is not nearly so concerned with describing facts as with creating images. All rights reserved.