The Atwood Comfort Control System thermostat uses a remote (called a Zone Control module) to actually control the furnae and a/c, especially where the furnace is tied to the heat pump (auto switches to furnace if heat pump can't do the job). The unit you saw in the a/c enclosure was probably the zone control. There is also a freeze sensor in the a/c coils to help identify when the heat pump or a/c freezes up and needs to be cycled off for a few minutes to defrost.
2004 American Tradition; 2014 Buick LaCRosse
Homebase in the Ocala Nat'l Forest near Ocala, FL