Why weren't the people underground affected by the nation-wide transmutation?
It could be because of how close they were to the center of the array, not just being in Central but being close to the actual point where the array was being activated from.

Remember in Xerxes Von Hohenheim didn't collapse when the nation wide array was activated because he was at the center of the array, not to mention the Amestris array must have been much larger than the Xerxes array so the "dead zone" of sorts was much larger.