Jove is composed of 42 planets that have collided with a 43rd planet. The 43rd planet is incredibly massive, and on its surface is a single H20 ocean with earth-like crust forming the sea floor. The 42 planets are studded into it, forming continents. The continents therefore rest on crust, not magma, and there are many places with 2 layers of crust on the planet. As a result the surface of Jove is incredibly uneven, with some valleys extending for thousands of miles, in depth or length. There are also enormous spaces beneath and between the continents, sometimes dry and sometimes flooded.
When the Prince discovers the huge cylindrical city underground, it is in one of these cave systems, and the eventual shifting of the Village Republic underground is only possible because of these enormous spaces.