Oftentimes I initially want to write "It's not that X, but rather Y" to mean "You might think I'm implying that X is true, so I want to emphasize that X is false; Y is true, and that's what explains my position," but I worry that this idiom is ambiguous; someone is likely to interpret it as meaning, "X might be true, but it's not the relevant consideration; my position is actually explained by Y (which does not necessarily contradict X)", which doesn't mean the same thing.