Can't imagine what could possibly do that while running. There is nothing for it to rub on. That said that is a really crappy casting. I can't believe they let that go out with that kind of porosity. I would have sent that right back to the foundry.
That's how they all are; even the stock turbo has the shaft nut like that. You might be able to make it out in the pic below... BTW, like Mitch said, that casting IS VERY porous... It is not affecting your performance one bit.
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