Yes, there were holes for the screws for the factory brackets as shown in the diagram. You're right... nothing in the directions says to discard the sleeve/bracket thing that came with the radio. But I did, and that worked out great. I guess it sort of clicked right away that the sleeve would make the installation miserable. I think that without the sleeve, the radio looked like the Toyota picture.
My factory radio was a double-DIN height, but Crutchfield included a small single-DIN pocket with the order, making the Sony radio (also single-DIN) + the pocket fit the vertical space exactly.
Looking at that Toyota picture for reference, I have the bare radio unit in the top half, and the pocket in the bottom half.