You are missing seepage with humidity. Seepage is the infiltration of water into the living space (basement) and makes the space wet or moist. It does cause concern about humidity, but seepage alone won't cause the humidity to reach the extent that is uncomfortable (for humans) and harmful for building materials. It needs to work with the elevated temperature at the location the ventilation is poor.
For example, the ventilation is usually poor in the basement, and it is usually moister than the living spaces above, however, in the summer, it is usually cooler than the living spaces above assuming there is no HVAC unit in either space. And at times, you even feeling chill, why? It is because the moisture has caused the air to saturate with tiny water molecules. When the water molecules hang on your skin, your body getting cooler.
The water molecules will hang onto anything in contact - walls, slab, ceiling, furniture, equipment, and piping. When the temperature is relatively low, they stay in dispersed form, you may feel damp, but no water can be seen. However, when the indoor temperature rises, the elevated temperature will lead to high humidity and causes condensation to form, a frequently seen phenomenon is the cold water pipes dripping in the hot and humid summer days.
The soil surrounding the basement is the natural barrier that provides ample protection against the influence of outdoor temperature and weather. As mentioned above, in the summer, the basement is usually a few degrees cooler than the floors above; and in the winter, the basement is a few degrees warmer than the unheated upper floors. But, the permeable soil can't block the seepage and moisture getting into the basement if the basement is not water-tight. So that's why we water-proof the basement wall on the exterior face, and provide the vapor barrier beneath the slab to cut off the water passages. For arid regions, a sump pump is usually not required, however, for locations with moderate to a high level of groundwater, it is advisable/essential to have a functional sump pump to relieve the groundwater pressure, and prevent standing water on the floor.
Finally, I don't want to compare the ancient people with todays'. They were smart to live in the spaces protected by nature (caves, underground houses), but they lacked the technologies and capabilities to make their living spaces even better, and that (bad living conditions) can be a contributing factor of dying young - living in a moist damp space hurts one's health, also, the moisture, seepage, gases, all carry bacterias, microbes, virus, and plenty of harmful substances.
My closing comment - a permeable basement is definitely doable, but not justifiable from any aspect.