In many shoujo manga, sexual harassment, abuse, and even rape is a plot trope. A common scene involves a boyfriend saving his about-to-be gang-raped girlfriend at the last moment, but the women are abused not only by antagonists but by their friends, co-students, employers, and future consensual partners. That's right, the men are forgiven and remain possible boyfriend material.
The women's response to rape by antagonist or protagonist varies. Typically, the women feel disgusted and dirty when touched intimately by antagonist, but find themselves enjoying the interaction against their will when the male protagonist is involved.
Even in consensual situations the women are rarely active participants. They almost never initiate sexual situations. In sex scenes, they lie passively while they are seduced and caressed by their partner. Women should seemingly be unconscious of their own bodies and resistant to the idea of their own pleasure.
Blackbird suggests that men in shoujo are physically potent while emotionally stunted, and women are the opposite. The man acts as the physical activator of the woman while the woman acts as the emotional activator of the man. For this example, imagine David Attenborough narrating: Enter popular male jerk. Enter sensitive outsider female. Female is sensitive. Male is shocked by her sympathy. Male is physically attracted to female. Male touches female (the level of intimacy of the touch depends on just how smutty the manga is). Female experiences physical attraction to male. After much unnecessary conflict, they live happily ever after.
This explanation covers the female protagonist's reaction to the antagonist as well. She has no conscious or unconscious emotional response to him. At whatever point in the plot, she may not have recognized her emotional response to the protagonist, but the author makes it clear that the emotions are coalescing in the background.
It would be interesting to contrast this dynamic to American romance novels. I don't have space to go into it now, but briefly, I think that the emotional/physical motivations are similar. The women are more aware of their desire and act more frequently on it, but it all starts with the physically/emotionally charged gaze that the protagonists share across a crowded room.