HARUKO HARUHARA SPOILER!
Haruko presents herself as connected to the Galactic Space Patrol Brotherhood, but the original OVA gives Naota very good reasons not to take anything she says at face value. Her real obsession is Atomsk, the Pirate King whose power she wants for herself. Naota matters to her because his N.O. channel gives her a way to reach him.
That does not make every interaction between Haruko and Naota fake. FLCL deliberately makes her harder to sort than that. She manipulates him, endangers him and plays with his feelings, but she also becomes attached enough that their final separation is not emotionally empty.
Haruko is funny because she refuses normal boundaries. She is dangerous for exactly the same reason. Whatever role she claims to be playing, she ultimately follows Atomsk.
HARUKO THROUGH THE ARCHIVE //
ATOMSK & MEDICAL MECHANICA //
Open page →Naota Is the Route · Atomsk Is the Target
It is not.
What she actually wants is Atomsk. Naota matters because his N.O. ability gives her an unusually powerful route through which objects, Medical Mechanica machines and eventually Atomsk himself can cross into Mabase.
That makes Haruko's relationship with Naota uncomfortable by design. She enjoys him, provokes him and becomes part of his life, but she is also using his body and his feelings to pursue something she wanted before she ever met him.