There's some truth to that. The issue though is what effect the small rise in heat exchanger temp has versus the effect of not heating two whole rooms. My bet is the change in efficiency by the increase in operating temp is small compared to savings from closing off the rooms. And we don't even know that any given installation is even at the max temp rise spec for the furnace to begin with. AFAIK, as long as you're within the max permitted temp rise, the furnace meets the stated operating efficiency on the label.