Saw this article today. It argues that there's a 'gender module' in the brain that even without hormone treatment is 'feminine' in transwomen's brains and 'masculine' in transmen's brains.
Transgender women tend to have brain structures that resemble cisgender women, rather than cisgender men. Two sexually dimorphic (differing between men and women) areas of the brain are often compared between men and women. The bed nucleus of the stria terminalus (BSTc) and sexually dimorphic nucleus of transgender women are more similar to those of cisgender woman than to those of cisgender men, suggesting that the general brain structure of these women is in keeping with their gender identity.
On the other hand, this article in New Scientist says the situation isn't so simple:
It’s unlikely that gender identity has such a straightforward biological explanation, however, and some studies have identified features of the transgender brain that appear closer to the natal sex, casting doubt on the developmental mismatch hypothesis. In a 2015 study from the Netherlands Institute for Neuroscience, a comparison of the distribution of gray matter in 55 female-to-male and 38 male-to-female transgender adolescents with cisgender controls in the same age group found broad similarities in the hypothalami and the cerebellums of the transgender subjects and cisgender participants of the same natal sex.
Neuroscience is very much in its infancy, and subject to preconceptions. I also think it's worrying that liberals are so keen on believing in natural mental differences between the sexes. That kind of thinking hasn't worked out so well for women in the past.