Components with a tall vertical space attached to multi-story buildings are used to assist natural ventilation, which however unavoidably results in different buoyant forces on different stories. To achieve equal flow rates on all stories, a dimensionless design approach was developed in literature. This study aims to examine the reliability of the dimensionless approach for designing the buoyancy-driven ventilation of multi-story buildings. Moreover, it validates the application of the approach to scenarios where the heat source strengths on stories vary. The experimental and numerical results confirm the reliability of the dimensionless approach for designing naturally ventilated buildings with uniform airflow rates and air temperatures on each story. In the case of a story with flexible heat flux, changing the heat flux affects the ventilation rates on all the stories. In particular, when the heat flux on this story is zero, buoyant ventilation continues and may even be observed on the third story. Furthermore, an increase in the heat flux on the first or second story enhances stack ventilation, whereas increasing the heat flux on the third story has a damping effect on ventilation in the other stories. Additionally, stories with identical heat fluxes had similar ventilation rates and indoor temperatures.