It's mostly a term of endearment, similar to how someone might shorten Michael to Mike, Jannet to Jane, etc. It is done to tease him when certain people do it. He's made a point of showing that he dislikes how feminine he is, getting annoyed at being called cute, having to make a conscious effort not to correct people, etc.
That's why at the moment not a lot of character's call him that, because they either aren't familiar enough with him to know how to get under his skin or don't feel comfortable doing so. There's a reason it's mostly the succubi calling him that.
It also stems from the plot being that there are very few men left in the city, hence why he doesn't bother correcting it or even introduces himself as Nat in some scenes.
In short, there's many different reasons to do it, though feminizing him isn't really the goal, the goal is to either show familiarity for some characters or annoy him for others.
As an aside, any content that comes across as feminization, such as his casual outfit and Rachael's comments about making him wear a skirt are either for plot reasons regarding the lack of men, as well as annoying him in the case of the clothes, or purely for humor.
There won't be any content that has him become more feminine in personality or start enjoying being treated as a girl. It will always just annoy him. It's almost purely for humor.
