I'm leaping in here as a cognitive neuroscientist, so I have some familiarity with the topic but I don't normally work on either brain structure or sex/gender
First, the journal is not Nature (the high profile one), this is Nature Scientific Reports which publishes anything that passes a basic threshold of being OK. So all sorts of stuff.
Second, the sample size (n=20 cisfemale, n=20cismale) etc is VERY small. most studies that look for sex differences should have sample sizes around n=100 per group, but I guess that is hard to find for trans samples. But it does mean that any conclusions may be unreliable. For example, the study showing no clear male/female brain differences had n=700 scans per group in the dataset (doi.org/10.1073/pnas.1509654112). When scientists report results on small sample sizes, we should always be very cautious.
Third, the whole-brain results show that transwomen are different to the ciswomen but not different to the cismen (the statistics don't allow you to say they are the same as cismen, but that is possible). A second analysis suggests that the insula is different in ciswomen compared to both hormone-naive and hormone-treated transwomen. The insula is commonly associated with interoception (feeling your body from the inside, ie, am I hungry, tired, aches & pains etc). None of the analyses suggest that transwomen are different to cismen, nor that transwomen are the same as ciswomen. But they also don't report any differences between cismen and ciswomen, so no general brain gender effects.
So overall, I don't think this study tell us much, and certainly I wouldn't take it as support for either gender-in-the-brain or something special about the brain in transwomen.