GPU is working fine.Looks like some sort paint/marking. If it works then it's not broken.
That's done manually?Thats typically a mark made by the QA inspector to verify the chip is in the right direction.
If its done by QA yes. They just hold a pen and mark them as they go through them. You will also often see them on electrolytic caps (though with a black pen), because if those are backwards they can turn into tiny little shotguns.That's done manually?