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The Cherenkov Telescope Array Observatory (CTAO) is the next-generation observatory for high energy γ-ray astronomy with unprecedented sensitivity and accuracy. Accurate estimation and mitigation of systematic uncertainties are crucial for its scientific performance. Atmospheric properties significantly influence both the generation and extinction of Cherenkov light generated by gamma and cosmic rays interacting in the atmosphere. This study provides a detailed analysis of molecular extinction processes, including Rayleigh scattering and molecular absorption, and their impact on the transmission of Cherenkov light. We examine typical summer and winter behaviour of Rayleigh scattering and seasonal and event-driven variations of the main absorbing molecules, such as ozone and nitrogen oxides, at the two CTAO array sites. Using simulations, we assess the effects of these variations on image intensity and trigger effective area, particularly during dynamic atmospheric events like stratosphere-to-troposphere transport. Based on our findings, we propose an atmospheric monitoring and calibration strategy to ensure that the CTAO meets its systematic uncertainty requirements, particularly for low-energy gamma-ray observations.