I don't think there's anything they need to explain about the phone call. It was just a way for Smith's Doctor to tell Clara that it'll be okay since she never witnessed a regeneration before, and he likely neglected to tell her given he thought it was his last.
As for the mention of the face, I think it was probably just acknowledging that Capaldi has been on the show before. Could be wrong, but it would explain why he recognizes his face.






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