There's a difference in childhood in brain structure:
Small, but detectable.
Reading the study, a number of points occur to me...
Somatomotor, visual, control, and limbic networks are preferentially associated with sex, while network correlates of gender are more distributed throughout the cortex.
I.e., the brain differences correlated with being trans are not the same differences as the brain differences correlated with being of the other sex. I.e., transwomen don't have "female brains"; what they have tends to be different from cismen's brains along some orthogonal axis.
we use the term “gender” to indicate features of an individual’s attitude, feelings, and behaviors
I.e., they're conflating gender, gender identity, and gender roles.
(4757 children, 2315 females, 9 to 10 years old)
I.e., the parents have had 9 or 10 years to observe sex-atypical behavior in their children
and react to it. If some "network correlate of gender" is caused by the child's brain being affected by the way the parents have treated the child, or is causing the sex-atypical behavior, the study would not distinguish those scenarios. I.e., it's a confounding factor they haven't controlled for. To tease apart those possibilities they'd need to do the brain scans in infancy and then wait 9 or 10 years and see if they still predict behavior.
Our models did not successfully predict the self-reported gender scores in either sex (all corrected P values >0.05).
I.e., their results on gender identity aren't statistically significant.
On the other hand, 0.56% (corrected P = 0.037; r = 0.08, corrected P = 0.033) and 0.55% (corrected P = 0.037; r = 0.08, corrected P = 0.033) of the variance in functional connectivity were associated with parent-reported gender scores in AFAB and AMAB individuals, respectively (Fig. 1C).
I.e., small, but detectable, as you said. Very small. The gendered-behavior signal is barely above the noise.
Our predictions of gender (beyond sex) are far less accurate than predictions of sex or gender alone, suggesting that gender may be a more complex construct that is not as clearly represented in functional connectivity patterns.
I.e., they can't reliably tell whether someone is trans by examining the brain, but they can tell whether someone is male or female. Yes, there appears to be such a thing as a female brain, but transwomen generally don't appear to have them.
His favorite playmates are: Her favorite playmates are: He plays with girl-type dolls, such as "Barbie". She plays with girl-type dolls, such as "Barbie". He plays with boy-type dolls such as action figures or "GI-Joe". She plays with boy-type dolls such as action figures or "GI-Joe". He experiments with cosmetics (makeup) and jewelry. She experiments with cosmetics (makeup) and jewelry. He imitates female characters seen on TV or in the movies. She imitates female characters seen on TV or in the movies. He imitates male characters seen on TV or in the movies. She imitates male characters seen on TV or in the movies. He plays sports with boys (but not girls). She plays sports with boys (but not girls). He plays sports with girls (but not boys). She plays sports with girls (but not boys). He plays "girl-type" games (as compared to "boy-type" games). She plays "girl-type" games (as compared to "boy-type" games).
I.e., the data on parents' evaluations of their children's gender-linked behavior was biased by arbitrary cultural notions of appropriate gender roles.