I believe you are reading the text too lightly. "Consensus reality shared by everyone around her" and "reality as all of Dani’s friends and colleagues knew it" is an explicit way to say that this was not "reality" but only what people believed was reality in the early 1980s.
I thought I understood what you meant by "set protocol." Now I don't. Could you tell me what it means? Why doesn't he get to set the protocol? (You may disagree with it, but that's different, no?) If not the author, who does? The subject? If the author is correct, then "post-op Dani was never offended in the least about being referred to as a man when conversations came around to her years of living as Dan."
The blog series is a historical progression of the evolution of computer games, with an emphasis on adventure-style games. It tries to place the reader in the context of the times, and include quotes culled from various references. At that time, she was known as the man Dan Bunten.
Consider the quote "(Speakeasy’s founder Brian Beninger: “Dan called out of the blue one day and spoke to Toni [Brian's wife]. She had never experienced an accent from the southern United States and had trouble understanding him…”)". Should the author rewrite the quote to use "Dani"/"her" instead of "Dan"/"him"?
BTW, are you basing your response only on the first essay and the single quoted paragraph from the second essay I linked to? Because the author goes into more detail which I didn't quote but might be relevant. Based on the paragraph previous to the one I quoted, I believe the author has decided the protocol will be to include a bit of explanation of future events, before settling in on a non-anachronistic telling. For example, Bunten is not the only important trans individual in gaming. Consider http://www.filfre.net/2014/03/10/ :
> According to Hales, it was he and another of Wolosenko’s favorite programmers, William Mataga, who planted the idea of doing adventure games in Wolosenko’s head in late 1983. (William Mataga had a sex change some years ago and now lives as Cathryn Mataga. I refer to her by her previous name and gender in this article only to avoid historical anachronisms.)
I think this is similar to, say, a history of Malcom X which covers the historical period when he was still called by his slave name of Little, or of "many young women [in the feminist movement of the 1960s who] changed their patronyms to more descriptive ones or dropped them altogether", quoting from Jo Freemen's description of her movement name Joreen.