A central lesbian relationship between Mara and The Woman in Black is depicted with agency and significance. The Woman in Black is a powerful figure, and Mara's choice to be with her is a key plot point. The film presents this relationship as an integral part of its surreal narrative, free from ridicule, condemnation, or harmful stereotypes, contributing to a respectful portrayal.

The film consistently subverts traditional family norms, depicting transient relationships, parental abandonment, and the eventual embrace of a chosen community over biological family ties, all within a narrative focused on individual spiritual transformation.

The film's core spiritual journey, emphasizing ego death, enlightenment through suffering, and detachment from material desires, aligns positively with fundamental Buddhist principles.

The film heavily utilizes Christian iconography and allegories, particularly with the protagonist El Topo as a Christ-like figure. However, it consistently portrays organized Christian institutions, priests, and religious figures as corrupt, hypocritical, or violent, critiquing the societal manifestation of faith rather than affirming its virtues.

The film's philosophical themes of cyclical existence, karma, spiritual liberation, and the guru-disciple relationship resonate positively with core Hindu concepts, though not explicitly named.