No Bra/WMG

Yuki is actually female-to-male, not male-to-female.
Yuki's just so feminine that everyone thinks it's the other way around. Masculinity and femininity have very little to do with gender identity, after all.

Yuki is a recursive crossdresser.
Yuki is a girl with a warped sense of gender identity who likes the idea of having certain people believe that she is really a crossdressing boy as she thinks traps are just so awesome and as a bonus, it also protects her virtue by keeping certain people confused about her.

Yuki is a Shape Shifter.
She is constantly switching between male and female because she likes to mess with Masato's head.