This is from a conversation in the movie ratings thread I had with someone else about the directors commentary and Nichols leading towards the reality aspect. I also posted the answers from Nichols himself from when the movie first hit...
It's a good commentary and he just seems to lean that way but from interviews he's been putting out as far back as Sundance he's open to the idea of people making different interpretations because whats being interpreted is irrelevant to what the movie is about. Here's a great answer from a Q&A
From Nichols...
Well, I said it last night in the Q&A, and I can reiterate here: His wife is the pivotal character. Michael Shannon is the main character, but Jessica Chastain is the pivotal character. Will she stay with him? Will she not stay? Will she support him? Will she not? The answer to that is the answer to this stress and this fear and, ultimately, the film. If this movie isn’t a film about marriage, commitment, and communication, what happens at the end, literally, doesn’t really matter. It can and hopefully will be interpreted in a number of ways.
As for me personally, I lean towards reality as well mainly because in every other dream sequence he's the pov character. In the end he's not. It cuts away from him several times and it's his daughter that noticed the storm, not him. The rain doesn't matter, it's just a design decision of what the storm would look like. The strength you hear in his voice at the end when he calls his wife's name to break her attention from stairing at the storm is just breathtaking. In just his delivery of the word "Sam" you feel his strength and control over the situation. The whole thing just completely took my breath away.