1. It's on the mainboard. It's the one with ATI written on it. Yes separate.
2. It will need a motherboard replacement as the chips are not designed to be removed.
3. They know which Wiis are under warranty from the serial number, it should not matter if you didn't buy it from new as the warranty is not person specific.
4. They'll know. Opening the case invalidates your warranty no matter what it's for. Nintendo are not dumn idiots, they know an opened for modification Wii when they see one.
5. They will swap it for a refurb more than likely. As I said swapping out IC like this is something that would be very costly and would be cheaper just to bin it, possibly after some fault finding.
But do consider that this is all just my opinion and is solely based on my own experience and knowledge gained.