There was a great online discussion of this but i know i'll never find it so i'll try to summarize from memory.

A) there is not much of a difference between mens and womens brains in structure or function. The few things that are genuinely different between the sexes (e.g. total brain size) are not different between men and TIMs.

B) There are small differences in brain function related to sexual orientation and as a lot of trans are also gay any study which doesn't control for this is worthless.

But more importantly:

C) If all brains are a mixed bag of characteristics, we would expect TIMs to have more 'feminine' brains and TIFs to have more 'masculine' brains. They've just got cause and effect backwards. You're comparing TIMs to "cis" women, not to women, so you're skewing your results before you even start. Assume that the brains of both sexes are equally on a simple spectrum from masculine to feminine. Then exclude the most "masculine" 10% of women (TIFs) and the most "feminine" 10% of men (TIMs) from the control groups. Now you're artificially created a difference in the average between the two sexes that didn't really exist, and when you compare the TIMs you'll find they of course have more in common with the women, while the TIFs have more in common with the males. That's the same criteria you used to pick the groups and subjects in the first place.

D) In order to argue that TIMs have lady brains you have to say "All women have X brain type, while all men are born with Y brain type. And when a man is born with X brain type it means - " record scratch you've undermined your starting assumptions. At best what these studies are doing is confirming that the brains of males and females both exist on a spectrum with at least some overlap between the sexes. Which...duh.

E) If it was possible to use a brain scan to tell someones identity it would be required before undergoing transition, and those without proof of "ladybrain" would be denied hormones and surgery. The same way if my cancer test comes back negative I don't get chemo anyway just on my say so. They can't have it both ways, it's either a physical condition or a spiritual belief.

F) Brains are plastic. If you take half of all kids and teach them engines and the other half baking, don't be surprised if you can pick up some small average difference between the groups. TIMs are typically forcing themselves into the same female stereotype role that is forced on all women and girls, so it's not weird if they share some small average difference in a particular trait.

And all of this is besides the point. I'm not saying a TIF can't genuinely feel girly inside his brain, I'm saying that doesn't matter one little bit to anything. He's still a man.