Thank you for posting this. I, too, do not accept the author's logic. As a general rule, it is simply polite practice to refer people in the way they wish to be described. In this case, Manning has explicitly stated a preference:
I hope that you will support me in this transition. I also request
that, starting today, you refer to me by my new name and use the
feminine pronoun (except in official mail to the confinement
In this case, it seems clear from context that "starting today" means "please start doing this thing now," not that pre-transition acts should be described using masculine pronouns, as DVK insists. The phrase "starting today" is explicitly present to indicate that the request begins immediately, not after any legal formalities, medical procedures, changes in dress or appearance, or anything else takes place. It does not mean "starting today, please use masculine pronouns when talking about the past." It would have said that if that's what it meant. I'll note that DVK seems fine describing pre-transition actions with the name "Chelsea," but balks only at the pronoun. This doesn't make sense.
Beyond that, this community is far from the first to address this question, and a number of style guides have arisen. GLAAD's style guide is in wide use. It says:
Use the pronoun that matches the person's authentic gender.
A person who identifies as a certain gender, whether or not that person has taken hormones or undergone surgery, should be referred to
using the pronouns appropriate for that gender. If you are not certain
which pronoun to use, ask the person, "What pronouns do you use?"
They also address this specific situation:
DO avoid male pronouns and Caitlyn's prior name, even when referring
to events in her past. For example, "Prior to her transition, Caitlyn
Jenner won the gold medal in the men's decathlon at the Summer
Olympics held in Montreal in 1976."
This style has been adopted by major media outlets, outlets that have taken good care to get this right, and these organizations have used female pronouns. If this was not the preferred style, Manning's representatives (and trans activists) would have made their views known in the past several years. As an example of this, the New York Times today used female pronouns to describe past events:
She copied hundreds of thousands of military incident logs from the
Afghanistan and Iraq wars
The same guideline is used on Wikipedia: "This applies in references to any phase of that person's life, unless the subject has indicated a preference otherwise." That page also makes a helpful analogy to changes of name. If Betty Smith graduates college and later changes her name to Betty Miller, it's still standard practice to write something like "Miller graduated with a degree in Art History in 1975," even though she used the name Smith at the time. Similarly, one can easily write about past events in Manning's life using female pronouns, even though she used male pronouns at those times.
TL;DR: the standard practice should be to follow the style used by major media organizations and always use the pronouns consistent with an individual's gender identity unless the subject has stated another preference.