I do not like to use the term "soul", because that implies some mysticism, but i'll just use it as a shorthand term here. I don't personally think of a trans woman as a woman, and I think there's no evidence to validate that notion that is scientifically observable. Every specific argument to the contrary, strikes me as dishonest. However, while there is no way to scientifically validate the notion, unlike with your age, or race, there's no way to scientically invalidate it, because of this truly baffling mystery, about how we can tangibly recognize a human soul. We understand perfectly, that it is your brain, which dictates your experience with memories, and experiences. Once your brain is no longer functioning, any memories, or experiences are going to be gone. However, when we talk about your brain, the key word there is "your". we don't think of your brain as one and the same with you, but rather a tool that yourself has. Humans are made up of sums, and all the sums, including the brain, are still just sums, which make up the whole that is your person. We have no ability to point to an observable aspect of a human organism, which can be seen as THE person, rather than something the person has. Again, while I don't like the term "soul" because I don't think the explanation is mystical, it is slightly scary that a consciousness can't be witnesses.

as your consciousness can not be witnessed, you can disassociate your physical traits, from the phenomena that is your "soul", and the claim that your gender is distinct from your biology, does not try to conflate them. Claiming your a different race, is a claim about your skin. Your skin can be observed.