Because nearly every character involved in the main conflicts (spell card duels, "incidents") is female, gender is largely rendered irrelevant as a descriptive or prescriptive identity. Characters' strengths, weaknesses, and motivations are individual, not tied to their being a woman. There is no male standard to which they are compared or by which their roles are limited.
Female characters hold all positions of power, agency and authority in Gensokyo, including the heroines and the "villains" (who are often just those causing "incidents"), leaders, and decision-makers. Their conflicts and resolutions are not about vying for male approval or breaking free from patriarchal oppression; they are about their own motivations, desires, and conflicts.
The absence of a prominent male presence means characters are not defined in relation to men, leading to a "gender-apathetic" world. In this environment, every character's strength, emotional depth, or personality is individual to them, rather than being a "female" trait. The typical power dynamics and gendered expectations seen in other media (where female characters might be assigned more traditionally feminine roles like mages or love interests in an all-male cast) are not present.
The approach allows for a wide spectrum of personalities and behaviors that challenge traditional expectations. Characters can be aggressive, passive, leaders, scholarly, or cowards, with their characterization stemming from their individual traits rather than adherence to a gender stereotype.
ZUN explained that he simply found a female-only cast fit the "aesthetic" of a bullet hell game better, suggesting that the precise, flowing movements of danmaku gameplay have a "feminine aspect" to his design philosophy. It was a practical design choice, not a deliberate political statement.