They changed the shape of the intake manifolds slightly on the ones that have EGR. I don't know why, they just did.
Also, around 97 they must have run out of intake manifolds that didn't have the spot for EGR to bolt to. So on the manuals they just made a block off plate that bolts on there instead. That way they just had to make one style 2.2 intake mani, and bolt on the block off plate if it was for a manual.