I've only had time to take a quick look at this, but I'm not sure the highlighted conclusion accurately conveys the main finding.
Most brain research in this area has confounded GD/trans identity with sexual orientation, which is correlated in the case of early-onset GD.
This was discussed by Cantor in his analysis of a Scientific American article. "Biological males and females differ from each other on certain subtle, non-learned features of the brain and body, and some samples of transsexuals are in-between on these features. That is, they were shifted away from what is typical for their sex-at-birth and towards the other sex." However, these shifts, such as 'click-evoked otoacoustic emissions' are also seen in association with sexual orientation which was confounded in the research.
The current study you linked states 'After controlling for sexual orientation, the transgender groups showed sex-typical FA-values.'. In other words, the study did control for sexual orientation and found that
after doing so there was only one brain circuit that distinguished the transgender groups. This circuit is one that relates to self-perception and body perception (and is also implicated in conditions such as body integrity dysphoria/body dysmorphia). At least one other recent study that addressed the confound with sexual orientation also found this.