Answering "No", to this question will not result in the entire module being scored zero. This is because the facility has (or should have) a valid permit, which is a requirement in the Site Info and Permit section for Environmental Permits. Since this is a Level 1 question, you will not be able to move to Level 2 or 3 if you do not answer Yes or Partial Yes to this question.
Not working within the limits in the permit is not taken into consideration in the FEM, as this is the responsibility of the relevant authority to enforce the permit requirement, and the Module or the verifier cannot take any action on it.