Would you expect an author to disregard all of the conventions we've discovered and codified through specified language because it's just "more natural" if they let it flow out of them? No, I don't think you would. You'd find it difficult to read and interact with, both as a reader and a fellow writer. Music is the same.
Music theory is just the natural language definitions of the sounds we hear. A composer is absolutely thinking in those terms and using them to construct the piece they hear in their head. It gives you a way to communicate, with words, the sounds you are hearing in your own head. It does not constrain music in any way.