I think this is a case where the theory of evolution feels pretty handy-wavy and doesn't answer the mechanism of how this happens. The article even talks about "bioengineered" silk! There are certainly lots of cases of evolution, so it is clear that things do evolve, but the problems of a theory are revealed in the edge cases, and I think this spider suggests that the theory really needs a lot of work to be a robust theory. I don't think a simple gradient descent (evolving toward more fitness) has explanatory power in this case. A theory that hand-waved around edge cases like this would never fly in Physics; at best it would be considered a holding theory until a better one could be found, like dark matter.
(Plus, I think it's fun to think about bioengineering in a sci-fi, or even Babylon 5 way)