I mean, if you believe the holy spirit put a baby in Mary, is it that hard to believe the holy spirit ensured there was a Y chromosome?
Most denominations of Christianity don't put much emphasis on the virgin birth. Immaculate Conception, the idea that Mary herself was forgiven of Original Sin when she was conceived, is the more important bit.
Just to throw some old testament in to the mix - in it, god is non-binary and/or gender fluid, as they use both male and female pronouns (Hebrew doesn't have neutral pronouns), and both man and woman were made in their form.
