This may be easier to understand by using a comparison. When I talk about the Muslim prophet I say Muhammad. However, many Muslims would say Muhammad pbuh (peace be upon him). This isn't that problematic, but let's say they the term was Muhammad ttp (the true prophet). Now I as a non Muslim believer would never use ttp because that would be insulting for whoever I believe in. If SE required that whenever I mention Muhammad that I append ttp, I would refuse as it would be extremely offensive to me.
Similarly by referring to a person with XX chromosomes as she, is offensive to people who believe that genders cannot change. A reasonable compromise would be to let whoever is righting chose what they want, or even allow gender neutral pronouns. But what SE chose to do was to say that people who believe that XY is a guy are wrong and deserve no respect for their beliefs.