Even with all the hormones, therapy, whatever, they still are, down to the base code in their DNA, a genetic male. That said, there is nothing wrong if someone wants to IDENTIFY as the opposite sex, and sees themself as a such, thats entirely fine. Hell, they can identify as a kitchen appliance for anyone cares. More power to them.
I chose this snippet of your comment, because it illustrates perfectly, the basis of the problem.
You, and many others, aren't even aware that by calling her a genetic male, are, in fact, being transphobic.
Let me explain, without any aggression.
You are confusing Gender with Genetics. Gender is a mental construct. The Genetic part could be whatever. The part that actually matters is the construct, it's where Identity is formed. Most of the times it aligns perfectly with Genetics, just look at that family, 4 children, only one had an issue with non-conforming construct. Gender dysphoria happens when the alignment is too out of whack. Like in Alex. It has NOTHING to do with chromosomes. It has ALL to do with her mental construct from where she derives her identity.
That's the reason why, Gender Dysphoria is diagnosed and ultimately treated by Psychiatry. Before you even come at me with "it's a mental disease", no, it isn't. It's a condition. There's no CURE. Even the Gender reassignment surgery is a stop gap, that helps correct the external aspects, but in some harder cases, the dysphoria can lead to deep depression and suicide.
What transphobia does is picking on a crippled individual and beating them up, because they don't conform to the transphobic person expectations. Newsflash: They also don't conform to their own expectations that's why they are trying to correct it.
So, when you type 'her' you are actually driving home their dysphoria, it's akin to slapping her in the face, or probably even worse. The thing is, the dysphoria may have multiple origins, but none of it is their fault. That "kitchen appliance" quip, says it better than anything else. YOU, simply don't recognize her RIGHT to affirm her identity. You want to force her to conform to YOUR expectations based on the external aspect of her body.
You may be less aggressive than others about it, BUT, all your arguments and speech say EXACTLY the same, even uses the same vocabulary. Do you want me to do the same that you do and say it looks like a duck, quacks like a duck, IT IS A DUCK, in this case a transphobe? Apparently you don't. That's the same for people like Alex. They may look externally like this or that, but, in their core they feel that they are whatever else. They are unable to correct their dysphoria, you however, can adapt and overcome.
Hopefully this is readable.
Peace