If it works well isn't it not similar to phrenology?

I think the implication is it doesn't actually work well. Running hard-to-explain models on brain scans has a history of producing papers which fail to reproduce, there were a bunch of bunk results in fMRI research a few years ago.

Exactly, it's going to turn out that it didn't work well but it will still get used harmfully.

While skepticism is healthy, I don't understand how you can say with certainty it will not work.

A hypothetical technology that could very accurately determine the sex of a brain would seem to be a boon for transgendered people. Early detection could mean better treatment and less suffering with fewer cases of desisting.

I do hope for your optimistic scenario, but I do not expect it.

It would be much more likely to reveal that the idea of a "female brain in a male body" or vice versa is incorrect.