Sir, what are the loads supplied by the ATS? I believe it is not intended for the whole electrical system as you're saying that it is directed toward legally required systems.
From my point of view, you are referring to another service disconnect that is intended for legally required system. If that is the case, NEC 2005 230.82 (5) allowed "Taps used only to supply load management devices, circuits for standby power systems, fire pump equipment, and fire and sprinkler alarms, if provided with service equipment and installed in accordance with requirements for serviceentrance conductors."
If the ATS is not rated as service equipment, then it is not allowed to connect ahead of the service disconnect, but if the ATS is service equipement rated, then it is allowed and you don't need the succeeding service disconnect as the ATS rated as service equipment already serve the function of the service equipment.