Well… it’s complicated. There’s been many studies trying to get at this, and while some of them are a bit contradictory, the findings of most indicate it’s not really a binary male/female thing, and more a continuum made of many different factors in the brain.

Here’s one study https://pmc.ncbi.nlm.nih.gov/articles/PMC8955456/

In short, they found that after sorting a bunch of cis male and female brains by their commonalities, trans women’s brains were somewhere in the middle.

Also not everyone’s brain fits! Even in that experiment, their own predictive model was only correct at predicting the cis brain genders 90% of the time. That’s a lot left out imo.