I'm probably looking too much into an insignificant detail, but here's my theory on Masumi Sera. First, some background information on genetics:
Asexual organisms (mostly single-celled organisms) reproduce through a method called Mitosis, in which the chromosomes of a cell are doubled before the cell splits in two.
Organisms that produce sexually, however, use a method called Meiosis. In human beings, the typical cell has 23 pairs of chromosomes, or 46 in total. During Meiosis, a cell simply splits into smaller components known as gametes. A gamete has 23 chromosomes in total, with no chromosome pairs. Whenever a male gamete and a female gamete combine, they form a zygote. The 23 chromosomes from each parent combine so that the zygote has 46 chromosomes, or 23 pairs, one pair from each parent. The first 22 pairs of chromosomes are called autosomes. However, the 23rd pair, which determines sex, is known as the allosome/sex chromosome pair.
A woman only has the XX allosomes, so during meiosis she can only donate an X pair. This is why all people, male or female, have an X allosome. A man has the XY allosomes, so he can donate either the X or Y chromosome, leaving a roughly 50/50 chance of the offspring being a boy or a girl. The default human gender, then, is female, but a single Y chromosome will result in male offspring, even if he has allosomal trisomy XXY or allosomal tetrasomy XXXY.
So, whenever an embryo is conceived, it will either automatically begin development of a female phenotype (if XX) or begin producing Androgens, which will prevent female development and begin male development (if XY).
However, it isn't always that simple. There are two conditions that can turn this whole equation upside down: Complete Androgen Insensitivity Syndrome (CAIS) and Swyer Syndrome. Under these two conditions, an embryo with an XY karyotype will not halt female development or begin male development. The end result is a phenotypically female person with the karyotype XY. These people will be born and raised female without knowing about their male DNA. However, they are not "perfect" women. Their bodies will not produce egg cells and they might not ever go through puberty (resulting in a totally flat-chested woman).
My theory is that Masumi Sera has either CAIS or Swyer Syndrome. If she has knowledge of this, she might not feel like a "real" girl, which would explain her boyish behaviour.
Again, I'm probably thinking too much into an insignificant detail, but what do you think?