I was of the impression that the art that shows Tut with the Aten was made before he became pharaoh, maybe even while Akhenaten was still alive. Then the old religion came back into style, and all of the Aten-related objects, like the throne, were kept around because they were too pretty (and too expensive) to throw away. The priests probably came up with some theological explanation to justify it, saying that the Aten had become part of Amen-Ra, or something like that.
Yeah, definitely. There is at least one object in the boy king's tomb which has his old -aten name, and there's the major monument of his reign, the colonnade at Karnak, which was later recarved with Ramses II's cartouche.