This study answers a practical question in renewable ventilation design: where does the exergy go when solar–geothermal preconditioning is combined with latent thermal buffering? A hybrid ventilation system coupling an earth–air heat exchanger (EAHE) with an air-based photovoltaic–thermal (PVT) unit is investigated, where phase change material (PCM) is embedded around the buried duct to act as a thermal buffer. Rather than reporting only annual energy savings, the work provides a risk-aware irreversibility breakdown that tracks exergy destruction across preconditioning, mixing, humidity control, and final conditioning. Several scenario analyses are conducted using hourly meteorological records collected over the 2019–2024 period. A bi-level optimization strategy is employed to simultaneously refine the system configuration and time-dependent operating conditions, including ventilation intensity and fresh-air intake ratio. To reduce occupant discomfort under critical conditions, a conditional value-at-risk criterion is incorporated to account for extreme thermo-hygrometric situations. The results indicate that PCM integration lowers system irreversibility. This behavior is mainly attributed to decreased ventilation demand and lower fresh-air intake. As a result, exergy destruction caused by air mixing and dehumidification is reduced. Although CVaR slightly increases during limited hot periods, overall discomfort risk remains about 50–60% below the baseline.