it totally depends on how she personally identifies, really. gender identity is wired in the brain, but i do think perception of that wiring also plays parts in it.
if she just feels she's more typically masculine than feminine, but still identifies as female, she could easily be fully mentally female and just a bit more masculine and less feminine than most. though i have no idea how it makes sense, it seems like some people also attribute excessive emotion/instinctual tendencies to women and logic to men, so if she feels that way about those tendencies, she may just be a more logical, less emotional woman.
transgender really refers to anyone who's not cisgendered. cisgendered = having your mental gender identity and physical sex matching, while transgendered is anything else. people might also be transsexual and prefer to have their physical sex surgically corrected to match their mental gender. but, some people can also be transgendered and be okay with their body as it is. if she identifies as mentally male, (s)he still might be fine keeping female anatomy, and even presenting as female, since some people are like that.
there's also another subcategory of genderqueer under transgendered, which consists of people mentally a combination of male And female. they might have atypical preferences in gender expression and/or prefer to have mixed gender-specific anatomy, or even no gender-specific anatomy to varying levels. but, they might also be mixed mentally male and female, but prefer a singular gender expression, and present themselves physically and/or socially as fully male or female.