It's a mystery to everyone.
Origins of the Gag Article
Yoroi Mikoto originally filled the role of "male friend side character" in Muv-Luv Extra as per standard visual novel cliches. What cast doubt on his gender was the confirmation of a female Mikoto in Unlimited/Alternative where everyone kept their original looks and gender, and several events in Extra that, upon deeper thought, cast even more doubt on Mikoto's gender.
Will we ever find out the truth? Or is a trap fine too? Inb4 sick fuck