While I am not well-versed in the particulars of the question (a.k.a. how the creation of the ontological western world pushed aside other non-binary ideologies), I can comment on the theoretical underpinnings of the inquiry. In his book, We Have Never Been Modern, Bruno Latour (1991) raises the point that one of the premises of the modernist agenda (born out of the western tradition) is the purification of world into neat categories. What this means is the creation of a classificatory system that allow us to organize the world into distinct, often dichotomous, labels. The first binary created by the modernist is that of the non-humans/nature vs. humans/culture. The male/female binary represents another level in such dualistic philosophy. Thus, because the modernist view has its roots in the west, it can be argue that following along the spread of western imperialism, was the spread of the binary purifying agenda.

For example, in some areas of Mesoamerica, the male/female binary can be understood more as a continuum with more categories than as neat labels. Often, gods had male and female components at the same time. Also, in the Isthmus of Tehuantepec, Oaxaca, there is a third gender called the Muxes that is neither purely female or purely male but a combination for which the modernist binary lacks the ontological background to understand. These traditions suffered after the conquest, because they went against the beliefs of the Catholic Church, the most prominent western institution in Colonial New Spain. Since the Catholic Church was very successful in converting people, once Mexico is created as a catholic estate it assumes western binaries as given and pushed aside prehispanic ontologies. So, to answer your question there is definitely a connection between the expansion of western imperialism and the male/female binary. What anthropology very often reminds us is that there are more than one way to classify and experience the world. I hope this helps.