For example, if you're reading a history book and a passage talks about how the imprisonment and torture of a captured combatant caused him to transform into a wild animal

I would 100% assume that it's a metaphor since humans don't turn into wild animals.

While the intent of the comic book and the history book are different, and the writing styles are not the same, the method used to determine if the message is literal or metaphorical is still the same. So the question still stands.

the question is answered by it being a completely different text. when Mystique turns into an animal I wouldn't assume it's a metaphor since I'm reading a comic. if I'm reading a history book and someone does something supernatural I don't believe it and would assume it's false. obviously this is different for religious scripture. like I already said, we don't read sacred scripture the same way we read history books and comic books. maybe you do, but most don't.

if you're asking "how do you determine what's a metaphor?" the answer is by reading it. not so easy with the bible tho when everyone you turn to has a different interpretation of it.