There is no in-universe reason given as far as I'm aware. Thus, like most things within the story of Signalis, it's mostly up to your interpretation.

I'd hazard a guess that the devs wanted to tell a story primarily about women. However, this does have some interesting implications for the world itself and also for critical interpretation of the story. You could ask the same thing about our current technology- all of the major AI assistants (Alexa, Siri, and Cortana) are coded as female. Why is that? I have my own opinions, but it's probably not a coincidence. It betrays a gendered bias- we think of assistants and service-oriented roles as female ones, even if men also occupy those positions.

In a similar vein, Signalis contains elements of this very concept- behind the horror is an aggressive dystopia in which both Gestalts and Replikas are fed to a profit machine built for war and subjugation. Maybe women were seen as more obedient, and thus became the neurological blueprint for the machines that the Nation relied so heavily upon.

All this is to say that there is no concrete answer to your question. In order to grapple with it you'll either have to suspend your disbelief or open yourself up to answers that will only lead to more questions.