Well, now you've got me wondering too! Mine came from the dealer with the filter sandwiched between the cover and the guide, PN 12 in the drawing. I always put it back the same way. The parts Manual shows it exactly the same as Stadium's illustration, not real surprising since that is where it came from.
I always assumed that the guide was meant to trap the foam into the cover so it could not move, and the seal was against the sides of the cover wall shaped for it. This makes sense to me from an airflow perspective, i.e. that the foam does not fit as tight against the airbox sides and will let dirt in around the edges, so I am going to continue doing it this way. I suspect the drawing is wrong and no-one ever caught it, or they just didn't want to reprint the whole thing for one little mistake.
Now I'm going to have to go out and have a look! It probably could use a cleaning anyway.....
EDIT: Disregard this post entirely!! I just went out and checked mine. It is exactly as the Parts Diagram shows: foam lays on top of the guide, which pinches it against the inner rim of the airbox, not against the cover, which has no rim. That's what I get for trying to figure this out from memory....a very poor memory anymore... I just didn't want to get wet on the way to the barn....still raining here after two weeks!!
But on the positive side, it DID need cleaning! One small caveat: there are several flat pieces on the cover that project above the crisscross guide. You are supposed to tuck the foam element inside them before assembling the cover to the airbox. If you just lay the foam against the screen in the airbox before closing it up, you may not get it properly seated. When removed, the inner rim in the airbox should make an indentation in the foam evenly about 1/4 inch from the edge....THIS is what makes the seal:
The tabs are visible in the right pic.