But the board in the 1000 isn't an original A1000 board, it's his GBA1000 custom board. If you're replacing the whole motherboard, you can do anything.
Not to say it isn't cool, but it's not exactly taking an A1000 plugging an '060 in.
edit: and at least a couple of people have hooked up '060 accelerators to their 500s. Internal would be tricky given the size of any current A2000 '060 cards, but definitely possible.