How do I change my ship's pilot?
Once you recruit your companions, they'll start bantering during Space missions. Andronikos is no different - had you not asked him to be your "pilot", you'd still hear his voice from time to time.
The one exception to this is that companions who don't speak basic (i.e., any companion that is subtitled, i.e., Khem Val) won't banter during Ship Missions. I'm not sure about companion droids like Scorpio. (2V-R8 and C2-N2 will never banter, despite speaking basic)