I don't think that it's implied that C:47 takes place after the WoA trilogy. We learn who the voice is in C:47, 47's creator, Ort-Meyer. Plus, there are plenty of references to the first few games in WoA, particularly in Mendoza which names several characters from the early games by name.
I think the more likely implication is that Ort-Meyer had ties to Ether and Providence, and that the asylum that 47 escaped from is now under Providence control. That would make sense, since they had knowledge of both 47 and Grey.
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