Following code snippet shows how these output variables are calculated

    for ( Loop = 1; Loop <= TotCO2Gen; ++Loop ) {
        NZ = ZoneCO2Gen( Loop ).ZonePtr;
        ZoneCO2Gen( Loop ).CO2GainRate = ZoneCO2Gen( Loop ).CO2DesignRate * GetCurrentScheduleValue( ZoneCO2Gen( Loop ).SchedPtr );
        ZnRpt( NZ ).CO2Rate += ZoneCO2Gen( Loop ).CO2GainRate;
    }

where ZnRpt( ).CO2Rate = Zone Contaminant Source or Sink CO2 Gain Volume Flow Rate [m3/s] and ZoneCO2Gen( ).CO2GainRate = Contaminant Source or Sink CO2 Gain Volume Flow Rate [m3/s]

Reporting during warmup convergence for timestep frequency would verify that ZoneCO2Gen( ).CO2GainRate is design generation rate multiplied by schedule value. And ZnRpt( ).CO2Rate is the sum of ZoneCO2Gen( ).CO2GainRate in successive timesteps. Also, above code doesn't take into account inputs from People or of GasEquipment objects. So even if CO2 inputs in these those objects are changed, it should not make any difference into above output variables.Agree though that documentation for the variables is confusing.