Here’s another take: Li’l Cheese is the child of Pinkie Pie and Cheese Sandwich. He therefore possesses unimaginable reality-breaking powers, and so qualifies as an eldritch abomination.
Now, eldritch abominations are impossible to comprehend by definition, but are often referred to with male pronouns for unknown reasons (for further information, see the discussion on Is Cthulhu a boy or a girl?). This is why Li’l Cheese is referred to as a “he” in the script.
Transexual gender nonconforming demisexual otherkin confirmed canon! Hahaha, bigots btfo! Pinkie’s child is LGBTBBQWTF, deal with it! Take that ponazis.
The script says one thing, the show says another, and the writers don’t want to commit to one or the other for the sake of “KEEPING IT AMBIGUOUS”, but it just comes off as indecisive stupidity.