As I understand it, the concern with too much flue gas CO is control of flue gas flammability. Do you have adequate analyzers to quickly and accurately determine the flue gas composition? There will be errors due to sampling location, analyzer delay, calibration uncertainty. The further you operate from the optimal region, the closer the furnace gets to being unsafe. How do you know the flue gas is completely mixed? Could there be pockets of rich gas that might light off in the convection section? If you do not have a fire or explosion where it is not wanted, then is that the definition of safe operation? Flue gas CO measurement is a tool to monitor how the furnace is operating. I've seen furnaces operate EXTREMELY rich so that the convection section was damaged. It is best to operate in the center of the road and out of the ditches. The burner and furnace design affect the optimal CO concentration. Your furnace will have a reference from when it is operating optimally. Sub-optimal operation indicates there is a problem somewhere.