I would think the meaning “X and Y are mutually exclusive” is the academic or formal reading of “All X are not Y”, while the colloquialism is the reading of “All X are not Y” as meaning “X is not a subset of Y (i.e., not all X are Y)”.
I would think the meaning “X and Y are mutually exclusive” is the academic or formal reading of “All X are not Y”, while the colloquialism is the reading of “All X are not Y” as meaning “X is not a subset of Y (i.e., not all X are Y)”.