With the total population of the Anzeans close to a billion, they only managed to fit a very small percentage inside their Mothership to escape their world to continue their race's survival.
That's why even though the Mothership had the size of a big city, most of the sections inside were filled with living quarters. It only had one Command Hall where the higher-ups of the remaining Anzeans would often gather or rather where they were getting their orders from the only Transcendent inside this ship.
The Command Hall was separated from the Operations Bridge. They're not engaging in space warfare after all.
The secret hatch that we used to enter from was located at the lowest deck. It was the deck where most ground weapons of the ship were located. It also served as the garage and hangar for their aircraft, spacecraft or smaller space vessels, ground vehicles and Pentacoms.