As you said, soldiers go with soldiers and civ staff with civ staff, but otherwise it's by choice. Since Penny isn't a soldier, her best bet would be rooming with Elizabeth, or with Jessica and Leon, unless there is a good reason why she is with a soldier (like Sunny needing to be near Engineering, or Atka needing to keep an eye on Ayame).Ah good, thanks Zombie. Compliments are always appreciated.
That said, who would be/would like to be roommates with her? Is there a system or something to determine that (besides "soldiers don't go with scientists etc") or is it just by choice?