I'm also waiting for the almighties one to come make fun of peoples being serious. They're always lurking in the shadows waiting for that
Personally I agree that in this particular case, the whole gender hiding situation is not meant to be malicious and it's just comedy.
However I can see why some people might find it concerning. I think the author was pretty aware of it too, and it's not a coincidence they made them kiss after Ookuma found out Kanda is a girl.
Despite that, I find the whole logic of "it's fiction and you are never supposed to read it a certain way/take anything seriously or view it from a real life perspective" faulty.
Because it's impossible to never talk about characters and a story from a realistic pov, or a moral lens.
Ironically, I've never seen anyone having a problem criticizing the morals of a story with, for example, cheating or how they dislike the behavior of a character. Why doesn't this "rule" apply there too? It seems like people only use it when it's convenient.