In an ideal scenario for you, how would you expect a situation like this to be handled? Let's assume for the purpose of the exercise that I did not have time to take note of, or fully describe every one of the character's assets if I were trying to describe this character to someone else. As it stands now, I would say "a naked man just walked past me on skywatch!".
In the way I choose to identify people, everyone is a "person" when I meet them. So in your example, it would be... "a naked PERSON just walked past me on Skywatch!"
If a person is going to get upset about being identified as a person, that person is not someone who anyone can have a rational conversation with.
Try it IRL when talking about people around you. For example, "See that person over there in the red sweater?" 9 out of 10 times, the person you are talking to will either clarify on the basis of race, presented gender, or both. "Oh, the black guy in Red?"
It's just the way people have been conditioned to identify and classify others.
To your point, or at least I think what one of your points was, it is very challenging for people with strong gender preferences to get others to react the way that THEY want to be perceived. In a way, that is a major part of what this topic seems to be about. Some players want other players to be FORCED to perceive gender identity in a specific way.
Given that, I think we're getting into a blurry area here and having to straddle a fine line between giving agency to some people without taking agency away from others.
Let's say I wasn't as enlightened as I am, and I see a character in the game with lipstick, eyeliner, a dress, cleavage and cock and balls. No matter what the other player might want me to perceive that character as, it's well within my agency to think, "Oh look, a dude with chick makeup." Instead of ... I dunno, a feminine expressing person, or whatever.
Ultimately, no amount of code or forced pronoun recognition or rules and regulations is going make someone think about someone else in the way that other person wants to be thought of. That's just not human nature. And it's not limited to gender identity. A conservative Christian might see themselves as a "righteous and pious upholder of everything that is right with the world" and I might see them as a "bigoted asshole with delusions about a big white man in the sky who cares about where they stick their dick"
My take away from this whole thing is:
The staff has done a great job of modifying the code as much as possible to enable a wide range of gender expressions.
There are some situations where genitals FORCE an associated "cis" centric pronoun.
Staff has made it abundantly clear that no transphobic or other derogatory remarks related to gender identity will be tolerated.
Right or Wrong, Like it or Not, 99% of the people in the world are going to see a penis and think "man" and see a vagina and think "woman". That's just the reality of things. It would be great if we lived in a more open minded and nuanced world. I know without a doubt that Sindome is more open minded and supportive of non-standard gender identities than society as a whole.