There are two significant factors that determine the rate of gas exchange. Surface area of the water, and circulation of the water.
It should make sense, that in order for gas to exchange between water and air, requires contact between the water and air. The more contact (surface area) the more gas can exchange at any one time.
Gas diffusion through water is slow. By having good circulation, you ensure that different water is always coming into contact with the air.
When people talk of surface agitation, they really just mean both of these things combined, since agitation of the surface water will increase the surface area of the water, an help to increase circulation.
When you slow the rate of gas exchange to reduce the amount of CO2 lost to the atmosphere, you also slow the rate with which oxygen can diffuse into the water. Life survives well with reduced CO2, it does not survive well with reduced O2. Better to increase the production of CO2 to offset loss to atmosphere, while maintaining good O2 exchange.