There are many reasons why someone might want to refer to another person using third-person pronouns when in their presence, and many legitimate reasons to use them when speaking of someone when they’re absent (and not all those occurrences fall into the category of “gossip.”) I talk about my students, other faculty and university administrators outside their presence all the time. It’s a daily part of my job. I suspect we all do, in our daily personal and professional lives.
Also, people who identify their gender as “non-binary” may or may not have typical chromosome profiles (who knows? Most of us don’t!) But you’re confusing a person’s gender identity with their chromosomal sex. Sex and gender aren’t the same thing, otherwise there would be no difference between “males” and “men” (and you only have to know about “boys” to see that’s not the case.) And physical appearances like “androgyny” and anatomical features like “Adam’s apples” aren’t always related to underlying genetics. Not all males have the secondary sex characteristic of an Adam’s apple and styles of dress and personal presentation have varied dramatically over the centuries when our underlying genetics (presumably) have not. Human biology cannot explain all those historical and cross-cultural variations, which is why we must also look to social, environmental, and psychological causes.
If these distinctions interest you, I’ve written about them in several other pieces on Medium: