Ohhhhh ok, I get it now. The WG cloned Vegapunk, and that explains why they were so easy about killing Vegapunk off - they have an obedient copy somewhere.
I was slow to pick up on this - I'm sure many of you put this forward already.
If I am interpreting the presentation here rightly, anyways. Though I might be wrong - why have the gorosei member come if they have a Vegapunk clone? Perhaps I am reading this wrong. But it would tie up a lot of loose ends, otherwise killing Vegapunk would be simply absurd.