The CO2 span is done in terms of the concentration, which does not change with pressure. Zero air has no CO2 or H2O, so pressure has no effect.
In contrast, the H2O span is done in terms of the dewpoint, which does depend on pressure. The dewpoint generator pushes an air stream at ambient pressure, saturated at the dewpoint temperature setting, to the AP200 inlet. The AP200 pulls a subsample of this air stream into the IRGA at low pressure. Changing the pressure does not change the concentration of H2O, but it does change the dewpoint. Because of this pressure change, the AP200 must calculate the dewpoint in the sample cell (at the reduced pressure). To do this calculation, the AP200 must know the ambient pressure (pressure in the dewpoint generator) and the pressure in the sample cell. The equations for these calculations are provided in Appendix I of the AP200 Instruction Manual.