It's always wise to avoid metaphors that can be interpreted literally. The problem is, in speculative fiction, that there's no such thing as a metaphor that can't be interpreted literally. Fiery hair really can start to strew sparks and smoke over the air. A growl can be the warning sign that your character is a werewolf (fantasy) or had a good chunk of wolf DNA engineered in (SF). Indeed, once or twice, I've grabbed a metaphor in a work and ran off to outline a story where it's literally true, and great fun it is.
On the other hand, you can work in associations that you can't get away with in mundane fiction. Your Dark Lord really can track death and destruction wherever he goes. Your wise old mentor really can live inside a tree. Or you can just suggest and hint these things are really in a manner that would be instantly dismissed as metaphorically in a mundane work.
So, you take what you like and you pay for it.
Metaphorically, that is.
Updated: Hmmm -- I should have mentioned this: You think that you can set up your world-building and then use the metaphors, as the reader will know by then?
The problem there is that you then have the style shifting in the book. Like changing genre or character, this can be very hard to do. Mostly, it causes a jolt to the reader.