Interesting, you can see where somebody in manufacturing started to cut the bottom out and then stopped. you have to wonder if a coworker saw it and stopped them before the cut was finished.
As far as the top piece if you look close you can see it is outside of the fins and there is a gap allowing hot air to flow up behind it and cause the bubble in the space on top of the refrigerator.
OP I would definitely create a new top seal that better blocked off the dead space. As far as the fin opening you should find the install manual online and see what the specs say. The manual will be very specific as to opening size and clearances from each side and back.
Which brings up another question. Can someone use some self stick foil ductwork tape (no not cheap $2 duct or duck tape) to seal all the edges of the baffles to the refrigerator? Or does the refrigerator put of too much heat?