Don't "joke" while praying is the lesson here. Assuming it was a joke. I have a hunch that of all the dumb wishes made, only that one was from the heart.
Not that Keisuke wants to be a girl per se, but envies how girls are less lonely or more openly affectionate with each other. What I find interesting is that Eito himself shares the sentiment. This premise could've very easily worked as well with Eito having been the one turned into a girl.
... while not likely to happen, I'd love it if the direction became Keisuke + Eito TS yuri (both of them being transformed by the end!) with Noel more or less left with nothing. But their childhood friendship being renewed nonetheless.
Anyways thank you for the TL, wyste! I've always loved your work.