I’ve tried to draft a post a few times, but keep getting stuck on various things that baffle me - so, I think all I can say is I sympathise, and I don’t really get much of it either.
There’s plenty of positives for both ways of writing, and, depending on the setting and how the game discusses gender, one may be better suited to a project than another, or it might just be up to an author’s personal taste. I do like that if authors include nonbinary characters in their gender-selection, it can result in more major nonbinary characters than are typically seen in a cast.
I also enjoy seeing gender-nonconforming characters, whether they’re selectable or not. (I always go hmmm, really? when I see things like “this selectable character was obviously intended to be a man because as a woman they’re too masculine” or “this non-selectable man may as well be a woman”.)
Like @AletheiaKnights mentions, I don’t love the system where selectable characters change based on PC orientation, because I might want to romance a man but not have every romanceable character in the cast be a man, etc.
I do have fondness for the patriarchy/matriarchy shift in Broadsides and Pendragon Rising… It was something I thought about doing in very early iterations of Creme de la Creme planning, but didn’t have the understanding/skill to figure out how I’d want nonbinary genders to work in a setting like that.