In short, you made a wall of text complaining about things that have been covered.
Ok, I’ll simplify. Finding that people born male can have brains that “look” female or vice versa challenges the very idea that brains can “look” either male or female at all.
Now, I’ll attempt to explain, in greater depth but hopefully still simply, why this is so.
You wrote that “transgender people…have a brain that looks more like the sex they identify as than the sex they were born with”. So, for example, a person who identifies as male but was assigned female at birth (whose “biological sex” at birth was female) would have a brain that “looks” male (and the same for someone born with/assigned the sex “male” at birth but identifies as “female”). In order to make a scientific claim that ANDYBODY can have a brain that “looks” female or male (regardless of what they identify as), one must first accept that there is sufficient scientific evidence supporting the claim that brains can “look” female or male.
Now, let’s say you are a researcher in cognitive neuroscience or some other relevant field here, and you’ve read a fair amount of the research on sex-based differences in the brain. You are more than aware, then, that one of the primary assumptions (perhaps THE FOUNDATIONAL assumption) behind this research (at least the research that supports the validity of claims that differences exist) is that sex is an independent variable. That is, all the research in neuroscience, cognitive psychology, medicine, etc., claiming to have found differences between male and female brains take biological sex as an unproblematic, binary classification from the start. So, for example, when claims are made that males have larger brains, the studies supporting this rely on participants whom they classify as being either male or female using biological sex.
Let’s say further that you find issue with the validity and interpretation of many of these findings (as various researchers from a variety of fields have). What would be one way to invalidate or challenge this body of research, from your perspective as a researcher in this hypothetical situation?
One method would be to find a decent number of individuals who were born with the biological sex “male” but whose brains “look” to be “female”, or vice versa.
In other words, you would greatly invalidate or challenge this body of research if you could find individuals with “brain{s} that looks more like the sex they identify as than the sex they were born with”.
Asking questions rather than jumping to long winding conclusions would have helped avoid such a blunder (such as, yes, they have studied the brains of cis men and women as well).
I know. I worked on some of that research (albeit not much, and most of the research I was most involved with here was back when I was still hoping to transition from physics to neuroscience and working alongside neuroscientists; since then its been mostly in a much more technical role regarding statistical methods and/or the physics of the neuroimaging methods used). I’d be happy to point you to some of the research relevant here, both with respect to the problematic claims underlying much if not all of the research on sex-based brain differences and with respect to how it is necessary for neuroscientists and those in related fields to move beyond these distinctions (or at least take into account less binary classifications for foundational assumptions and guiding principles).
What most of the studies that take into account perspectives from LGBTQ research or more generally research across fields that isn't based on a binary classification of sex that is all too often automatically reduced (in the main) to gender have found is that previous research was...faulty. In part for the very reasons I outlined: if you take as given that your participants can be classified as "male" or "female" according to biological sex, then you will be necessarily limited only to finding differences (or failing to) along these lines.
Any neuroimaging study that finds individuals whose brain "looks" to be other than their biological sex would be evidence against the validity of sex-based brain difference findings (of course, another set of issues emerges when one takes into account the brain-based changes among individuals who have underwent e.g., gender reassignment procedures, and there are other nuances, of course, but you already called me long winded so I'll spare you more details here).