Nothing prevents them from changing the rules, but if they are not consistent with anything that was pre-established in the narrative THEN the suspension of disbelief for the audience is subject to be broken. That is generally seen as a result of bad or inconsistent writing.
If Elves suddenly started flying or dropping out of the sky then yeah, people are gonna go WTF. And yes, Meteor Man is definitely a WTF moment but it's framed in a way where they intentionally leave it mysterious so we don't know who or what he is. If they confirm him to BE an Elf or Human then yeah, that would fuck up quite a lot of the established world wouldn't it? Right now, we don't know enough to even judge if he is, which is why the suspension of disbelief is still intact.
There is no case where anything goes just because it's a work of fiction and anything can be done at the behest of the Author at any time. That is where criticisms come in to specifically point out inconsistencies. Just like the whole reason Tolkien put this to paper in the first place, because Christopher Tolkien was pointing out inconsistencies in his descriptions in the color of Bilbo's door or the ornamentation on Thorin's hood.
I think I've made it clear why Meteor Man is not a good example of waving away internal rules of 'realism' just because it is fiction. Meteor Man doesn't contradict anything that has been established prior, because there is no confirmation of who or what he really is.