The board that he shows at 0:41 is the 4th prototype, aka the board that is now shipping to developers and backers.
The board he shows later in the video is the older prototype, which does have a different layout. I'm not sure why he uses this older prototype through most of the video, but I suspect that it's because he already had this footage and didn't want to (or need to) shoot that section over again, just to show a board with a few pieces in a different place.