Yes, and behavioral studies, genomics (and omics and bioinformatics methods), whole swathes of big data analyses on vast bioinformation databases, etc. Of course, most of these are more problematic and only indirectly measure variations within and among the populations of interest.
But the overwhelming majority of studies here involve neuroimaging technology & methods both structural and functional.
Let's accept this as unproblematic for a moment. The point you seem to be glossing over is that when "they" found this result "they" made the assumption that biological sex is independent of things like gender identity, culture, etc.
In other words, the research purporting to show that "men's and women's brains look different" assumes that "men" can be defined unproblematically by anatomical/biological sex, and the same with women. That's been a central criticism of the research, including criticisms from gender studies, women studies, etc., not just within neuroscience and the cognitive sciences more generally.
But once you assume (as this research does) that what enables one to speak of "men's and women's brains" is biological gender and nothing else, then the moment you assert that one can be biologically/anatomically male and have a brain that "looks female", you've erased or undermined the foundational assumption behind the claim that "men's and women's brains look different."
Think about it:
The claims about sex-based brain differences rest upon the validity of using biological sex as the sole determinate of whether an individual has the brain of a "man" or a "woman".
So, for example, under these assumptions it is impossible to show that an individual whose biological sex is male can have any brain under than that of a male. Likewise for women. It has been the guiding and foundational principle of research on sex-based differences in the brain that we can safely and validly assert that someone who is biologically "male" has a "male" brain.
If one then uses this research and finds individuals whose brains "look like" the sex they identify with, it means they do not have brains that "look" like they are supposed to according to the research claiming that men and women have different brains.
It is this binary assumption that is at the core of so many critiques of such studies in the literature:
Sex beyond the genitalia: The human brain mosaic
The Future of Sex and Gender in Psychology: Five Challenges to the Gender Binary (see attached)
Re-conceptualizing 'sex' and 'gender' in the human brain (see attached)
I'm not trying to argue for or against the body of evidence (or some part of it, as it is quite diverse) supporting the existence of differences between male and female brains. Nor am I arguing for or against claims about the ways in which gender can manifest differently from sex in those whose biologically assigned sex is incongruent/differs from their gender identity.
My point is simply that you can't use a body of research that has depended almost entirely on the assumption that the only thing that makes male brains "male" and female's brains "female" is biological sex (and therefore those whose identity differs from sex would be classified according to this binary system) as evidence for transgendered brains with claims that contradict this foundational assumption. You can, of course, undermine the notions associated with binary sex classifications and/or their relevance to gender with such research. And people have.
But there is a basic problem of logic at play here. You can't go from the assumption that "men's and women's brains look different" when the research supporting this ignores anything other than sex assigned at birth or biological sex to support claims about individuals who have brains that "look" like anything other than biological sex.
Such claims would have to be considerably more nuanced to avoid what is bordering on a proof-by-contradiction that it is indeed possible to both have established "men's and women's brains look different" while asserting that one can have a brain that "looks male" when one's biological sex is female.
Such dichotomous thinking. If you accept that the interaction between brain development, sex differences in the brain, and sex and gender themselves are all more complicated than simple reduction to biological sex, then you are rejecting a core assumption underlying a vast majority of research supporting differences between male and female brains.
But regardless, the truth is that we actually know considerably less about the supposed differences in male and female brains than has been assumed, and the advantage of more nuanced studies and transgender studies is in part that we are better able to question the methods, findings, and interpretations of findings of previous work as well as ask better questions, new questions, and broader questions.
Neuroscience in transgender people: an update