Humans once imagined that war was just a video game, where you sat in front of a computer, and fought the battle entirely with unmanned weapons.
For the Serpent People, this mode of warfare conceived by humans was a reality.
The mothership served as the vessel for numerous unmanned spacecraft, the manufacturing factory for monsters, and also the remotely controlled command center.
So after initially gaining control of the mothership, Gao Yuan and Ram coerced the Serpent People, who were lucky enough to survive, to send out unmanned spacecraft to transport people from the ground to the mothership.
Because of the mothership's immense size, it was simply impossible to land it completely on the ground; at most, it could only hover above the surface. And if it were to hover above ground, it might as well stay high in the sky and use smaller ships to transport people in and out.