As always, you're very brave to share your feelings especially on something controversial, and yes, they do matter. You love her and are clearly willing to do all that you can to support and be there for her. But most of us can see that with medical plans as radical and irreversible as this, huge doubts will creep in until you are able to see the changes that she seeks and how much of a difference her 'new' body will make to her mental health and her life.
If you can bear it, I would try to discuss it with her - not to try to persuade her against it but so that you have a better picture of how she really feels and some of the things which have led to this decision. Talking together will also allow you to become accustomed to something that's possibly quite an alien concept. It seems that this has been a long time coming and with her history of gender dysphoria and all the confusion and desperate unhappiness, it can't be a real surprise to anyone in the family that this is never just going to go away - without causing further serious problems in her life.
She must have thought so much about this and she must be so certain that this is what she wants. Maybe you will feel slightly better once you know just how committed she is. It's to be hoped that not only will she be followed and monitored and carefully assessed through a very long process, but regularly before each stage by psychiatrists specialising in gender reassignment. Obviously this is no flash -in- the- pan decision nor would it be allowed to be if all the necessary mental and physical health professionals are involved and she knows the full extent of what will be happening to her.
Like you, I would be so sad and sometimes quite desperate if this was happening to a much loved young person in my family. What might seem unnecessary surgery and all sorts of interventions on someone we love, someone that would outwardly appear to be just fine, is a horrible thought, but so is her feeling condemned to a very unhappy life in a body that continues to feel 'wrong'.
I was quite privileged to follow a young health professional whom I visited regularly when I lived in England. She was so very good at what she did and patients clamoured for appointments. We used to talk throughout my treatments and she would share her life plans. Then she told me what was going to happen, so I wasn't surprised or shocked when I saw her again with a slightly different hairstyle and a lot of facial stubble. She had gone to hell and back over many years of childhood, adolescence and her 20's, and through her training, just feeling that she'd never fit into society, never settle with a partner etc., I was astonished at her courage but it seems she had already had 'endless' counselling, endless support and advice and for each stage, careful monitoring and wonderful people to talk to.
It was amazing that over a long time (a couple of years at least), various surgeries and lots of recovery time, she stayed positive, was - she said - so happy to be on such a journey and, incredibly, never lost a single patient! She didn't bare her soul to all but not a single person commented on her changing appearance or even when she changed to a male first name!
The last I heard he had a partner, a nice home, a successful practice and a very busy diary of appointments, a great social life and is truly happy and settled. I wish the same happiness for your relative, her family and you.