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Mathematics is a limited way to describe nature - try counting a sub-atomic particle, it's impossible. It might be there, it might not - and as soon as you know whether it was there or not it's gone somewhere else (or has it?).
Physics and mathematics does a very good job of describing the universe in discrete terms that we understand - but we invented those terms, and chose how to define the boundaries between them. A feature of the universe is just that, a feature - something arbitrarily separated from the rest of nature by our minds. Mathematics help describe the relationships between those features we have deemed useful, but it's all invention piled on top of invention. It's real to us, but not necessarily so in the big scheme of things.
Why is the ratio aesthetically pleasing? It would help an animal distinguish the diseased from the healthy. A potential mate with limbs not fitting the Phi ratio may well be deformed and hence poor breeding material. It's not to much of a jump to guess that a system evolved to express such a preference might be implemented as a more general liking for things that posses similar proportions.
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