Wouldn't the people who know the physical things just write requirements for those farther on down the chain?

The threat analysts say, we need to destroy Iran's ability to make nuclear weapons. The nuclear weapons specialists say, the part where we can best do that is by somehow breaking their centrifuges. The centrifuge technician they call up says, "well, x RPMs will really ruin those things. And it would be hard to tell if they did it like this..." Then the software guys make the code that ruins the centrifuge, and the red team incorporates it into their fancy worm, with specs on what exactly to look for.

Ultimately, it was kind of a failure in that anyone found out about it. Maybe there were better programs, and because they were better we never heard about them at all. But still it's pretty amazing :)