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Giratina is completely androgynous, exuding no immediately identifiable masculine or feminine characteristics. Furthermore, Giratina is an emanation of a higher celestial entity, the creator of all things (within the context of Pokemon) that has no need to reproduce and cannot do so of its own volition. It is a unique creature, of which another can only be generated through the power of Arceus, the aforementioned creator of all things (within the context of Pokemon). Fabrications of Giratina can be conjured through the use of heretical devices such as PkHEX, but these fakes share the same traits as the real Giratina. They are androgynous and incapable of reproducing.
Zacian is different. It is sleeker than Zamazenta, its counterpart, and wields a sword, requiring much more dexterity than bashing things headlong with a shield. We can therefore presume that it fights with grace and because of its slender body and graceful movements, the culture surrounding it ascribed it a female persona in their mythologies.
Pic related is Yubel, a monster with both female and male genitals. It is a "perfect being" without gender, and the only appropriate pronouns are "it" and "they", even if they come off as a little harsh and impersonal. However, this monster is usually referred to as a female. People cite its affection for the protagonist, Judai, as a female trait, despite Judai's own homoerotic tendencies, despite the fact that the source of Yubel's jealous yearning is a man, like Judai. Despite the fact that, prior to becoming a monster, Yubel lacked a pronounced bosom like most females from its franchise, and instead had pronounced muscles. Despite the fact that all of the traits from the male side of Yubel's body are carried over from its human form.
tl;dr Giratina isn't a girl, and your waifu used to be a man.