The film lacks explicit LGBTQ+ characters or non-cisnormative identities. The narrative focus remains centered on socioeconomic and biological distinctions between the Boxtrolls and the ruling class.

Winnie Portley-Rind disrupts traditional hierarchies by acting with significant agency and intellect. She avoids the passive 'damsel' trope, driving the investigative momentum of the story.

The Boxtrolls serve as a sophisticated metaphor for racial and ethnic diversity. They represent a marginalized 'other' subjected to systemic scapegoating and social exclusion by humans.

The film offers a robust critique of Western institutional structures and aristocratic corruption. It deconstructs the concept of civilization by framing the Boxtrolls as misunderstood rather than deviant.

The Boxtrolls' unique physicalities and social behaviors can be interpreted as neurodivergence or physical difference. They are portrayed with dignity, though the focus remains largely on class allegory.