"Put another way--when one theory replaces another, it must be fully contain the previous theory."
This is certainly our hope and desire, but I think you're taking it too far. For example, if we took what you're saying as some sort of prescriptive rule that is improper to violate, we wouldn't have found quantum theory in the first place!
So I think it's important to allow proliferation of theories that explain portions of the evidence, because that explores the space in which we might hope to find a unifying theory.
This is certainly our hope and desire, but I think you're taking it too far. For example, if we took what you're saying as some sort of prescriptive rule that is improper to violate, we wouldn't have found quantum theory in the first place!
So I think it's important to allow proliferation of theories that explain portions of the evidence, because that explores the space in which we might hope to find a unifying theory.