Offer heating /cooling vents for the 3rd row. Perhaps they would only open when the 3rd row seats are in place.
This is sometimes available on higher-end large SUVs (usually in the roof) as an option with a separate set of HVAC controls.
This may be difficult to engineer, as there are no vent paths available from the front to the rear either on top or in the floor. It may be possible to have a separate HVAC system just for the 3rd row using thermoelectric techniques and a fan.