Well clean calories dont matter. Even if you mix skinless broiled chicken breast without salt, and have a cup of fresh steamed spinach with lemon, once you ingest it, your stomach will release Lipase and Pepsin to breakdown the carbs and protein. Instead of having the protein flooded with HCL and Pepsin to metabolize and digest completely, you have a mix of 2 chemicals that kind of offset eachother. You still digest it, but if you keep your carbs and proteins seperate, you will allow them to be broken down more efficiently without the presence of other foods and chemicals which may hinder maximum digestion and metabolization.
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