The few Mountains that are lucky enough to stand above the Vinefields are known as the "Free Mountains"
Originally the Free Mountains were dug into from their base and the mining went up, never actually breaking to the surface except to move air in small crafted vents. This eventually led to bigger cavities that led to more cities.
Because of this the lowest part of the mountains are now ruins of worn down cities.
After the invention of the Clock and the Bound were able to tell when it was safe to be exposed to open sky the Mountains were opened up to allow more ventilation.