The reasons for it:
1. Ostracised by society as a shut-in, she's an outcast, an "alien" compared to normal people.
2. Necronomicon is a grimoire with information incomprehensible to normal minds. A UFO is the same. Both meant to convey the "unknown," reflecting Futaba.
3. As the team's navigator, she has a "vessel" type persona (since she actually goes into her UFO) like Fuuka and Rise, but hers is cooler. The Necronomicon and a UFO also represent objects whose owners have information that other people don't have, which represents her abilities as the navigator.