(Someone created a thread for the series? Didn't know you could do that)
Vae does write quite the strange plot normally, frequently resorting to gender-heckery and the usual otokonoko business, and this is no exception. Though seeing "I'm good at pretending to be a girl, God, so make me a real girl please" in the
raws is maybe the
most explicitly stated gender-transition wish I've seen outside of Norito's "I wish everything was yuri" one-shot.
EDIT - I'll admit I embellished, but the original line in chapter 1 says
神様・・・可愛くて完璧女の子な僕を・・・ ほんとうの女性にしてください
To semi-quote another translator, this character outright describes themselves as a boy in an earlier page and here outright asks for a
sex change to become a "real woman" or to possess "the nature of a woman". (女性 vs 女の子)
In a later page (noted from the raws as well), Kuroyou lays out what was asked for and what happened.
And the script and visuals indicate that Kuroyou is angry in that her god of choice blessed the wrong person.
While one might make the argument ad nauseam that this is more about "taking away otokonoko" or whatever, it's not well-founded. Yes, there are going to be folks who might be upset in the story that someone suddenly would go from gender-bending AMAB who looks conventionally pretty to "holy crap I have a vagina now" and that "ruins the mystery" ...
Those folks are missing the point.
The math and chalkboard are there. Show your work.