I disagree with your premise on a few points, and because I have Holiday obligations I can't currently expand on them to my liking. Suffice it to say, for now, until I can sink my teeth into this discussion, that a writer who makes 'whatever' happen for 'any reason' is a bad writer, and a good writer that doesn't betray their own craft will be selecting the choices and words that make the most 'sense' and have the most correct, desired 'impact'.
Your premise is along the lines of saying that all paintings are pointless because the painter can decide the subject, the paints they use, the brushstrokes, the lighting, etc. While one might make the point that all art is 'pointless', this would be denying the truth that there is value in art, and this value is derived from a handful of attributes, both in what the artist instills and what the viewer/reader extracts from it.
If your argument is that 'well it's made up, ergo null', this is wrecked by the fact that a story can have consistent tone, themes, characterization, all of which could be used to convey a point, be entertaining, etc. Verisimilitude is but one aspect of a piece's value, and a skilful writer can achieve internal logic and consistency even in the most abstract fantasy works (like Michael Moorcock's Cornelius Quartet).
But, to cut away at the 'Writer is god' argument at the Gordian root, yes a writer is free to put whatever they want down. This does not in of itself make the work good. It reveals that the writer is, if they make these missteps in their own subject matter, that they are not familiar with what they are creating. And, if it is not good, and they are not able to perceive all factors going into the work, then it is not the work of 'a god'.