You are confused because you are seeing gender how it is currently used, which is a social construct that is assigned to people largely beyond their control that affects how others see and interact with them; and what some people want gender to be: solely an expression of one's personal gender identification, that to be respectful everyone else must acknowledge.
I'm actually not even going into how people want to identify, which I see as largely their own choice. I'm more interested in why we are supposed to change the past tense pronoun and name. Really, my question is the same when the pronoun argument is excised from it. Consider Cassius Clay and Muhammad Ali. Do we say Cassius Clay won the world heavyweight title in 1964, or do we say Muhammad Ali did, knowing he changes his name afterward. There are cases where it is more confusing both ways, but from a historical record perspective, it feels more correct to me to say Cassius Clay did, simply because that also denotes who he identified as at that point in time.