Brain scans in order to establish some gender profile is inherently flawed in the first place. The standard is based on a prejudice. Natal women don't have to pass a brain scan in order to establish their brains to be like a woman's, and no matter how a woman's brain turns out to be, that always just further establishes the mean, or standard. It is only transwoman that have to pass a test, and have to have their brains pass a standard, which indicates how female they are.
So, it is no surprise to me that everyone's brain is different, and woman taken as individuals, and checked against the mean thus often wouldn't pass the test themselves.
No matter what kind of profiling standardization test that one wanted to run, and check trans people against, the fact would always remain that the mean, the standard by which they were checked were always taken to be women, or men without having to pass some test -- they would always be founded in prejudice.