From my point of view you got two approaches here:
1 - First one, confront her bluntly and straightly. From what you describe your mom looks like (don't take it bad, please) some kind of bully/bossy/overbearing person. Usually this kind of person just regard as equals those who are just as bossy/bully/independent as them are and they look down a bit at those persons who they can control. So, one option, could be to rebalance statu quo between you, proving yourself in some form independent and impervious to her considerations and thoughts. Moving forward and doing what you want to do. There's a true possibility she wouldn't accept it either, so obviosuly this is kind of risky.
2 - Second one, move on stealth and slow (on her back) but steadily and consistenly. Find another therapist, made up some excuse, and go visit him on her back; eventually start HRT under new doc's supervision without telling her... Also make slow but constant moves to open up her comfort zone. For example we know she told you took too much from your eyebrows: ok, keep taking that much and eventually she'll get used to the new eyebrows, then, take a little more, wait for her reply, and keep on taking that "new much" and so on; this way you'll get a much larger comfort zone. Going slow but constant (no stepping back) on those things could help you in two ways. Firstly, enlarging her comfort zone would leave you a much more vast space and capability to be yourself: eventually wearing a girly hairdo, wearing very girly or androginous clothes, wearing make up, purses... etc. Secondly, there's a possibilty she would get it and accept yourself being a woman after viewing those consistent and continous things and how much you'll have changed. Of course this is not for sure, but even in the event of unacceptance, at least you'll end with more freedom to be yourself.
Anyway, key point is to start moving.