It's not the small and agile Logos that Niobe pilots through the cramped service tunnels, but this hulking beast.
Bugs disagrees with her as she is the young rebel that Niobe once was.
It was the smallest ship in the fleet and the most maneuverable, which is partly why it works out really well for Neo to borrow when it's time to confront the machines in their city, 01.
The Merovingian was the entire operating system on which the previous Matrix ran, so he was able to pull out subordinate programs and carry them over to the new Matrix.
We later learn that Neo subconsciously left his Modal open hoping someone would free Young Morpheus who would in turn find and free him.
Or, moreover, a powerful celestial being, known as the Seraphim.
In the third movie, Trinity pilots the Logos to 01, and the ship is destroyed.
It is a face sculpt that photographs nicely but disapoints in reality.