they're portrayed as a effeminate pervert (way too clingy, stalks MC's dad, "call me neesan instead of uncle" stuff).
It's a personality trait, it's not like other characters make fun of him for being who he is and make fun of his gender...
I think author is making fun of such personalities like always pursuing beauty and romance to the point of stupidity by pushing the personality to the extreme, but it's not like you need to have a specific gender to do that, don't you ?
Being a pervert isn't selective only to a specific gender either.
I feel like you dislike this character's intended behaviour, which isn't related to his gender at all ? I mean any person with this behaviour can get annoying regardless what their gender are, it's not that him being trans plays an even more important role in that annoyance, right ?
I'm curious what you think about theses thoughs of mine.