I have mixed feelings on the pronoun use, but having read some of her autobiographical writing I don’t think she would have taken much issue with it. This piece is more focused on her work in computer engineering, so I felt it was appropriate to post here.
What they “felt on the inside” is not the same as what they actually were at the time though. Referring to them as he or she is just a statement of fact at the time.
We had this same thing when Ellen Page became Elliot Page. Then there was an attempt to retroactively change all references and make them Elliot Page, even though the work he did before was as Ellen Page.
It’s not transphobic to acknowledge the person they were before transition.