"Hey, the VFDs are programmed to skip through this frequency band during the accel ramp to 25k RPM, but every once in a while they hickup and then the bearings rub. What's up with that?"
So it seems that there is one factory layout Stuxnet is looking for. I.e. it will know what point 35 is.
If the main fan control gives a fairly standard reading, it shouldn't be too difficult figuring out what the particular factory it has infiltrated has wired that point to, for example.
Also, I haven't heard any definitives on what kind of factory this is targeting. I do know that there aren't many companies that develop and design high tech industrial facilities. Despite StuxNet having infected thousands (millions) of personal PCs, it really is only looking for maybe a few dozen or so in the world that are of the right type. Combine that with a low number of factory designs, and it could very well have a pre-determined database of how its intended targets are wired.