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On a second (or ever third :)) thought I can imagine following dialog:
-- Где он? В Москве?
-- Нет, он не в Москве.
It implies that you know where he is but don't want to say. The only thing that...

Care to expand on that?

I understand the nom/ gen relationship with negation, but in this case it's not Он, the grammatical and semantic subject, that's being negated, it's в Москве. So why is the...

No, it's not correct ever though native speakers sometimes do use it. "Он не в Москве, он в Петербурге" is correct. But just, "Он не в Москве", is not. "Его нет в Москве", is correct.