I'm going to go against what most are saying because I've cooked I can't tell you how many shoulders on both the top and bottom grates.
The only real difference I see is being closer to the heat source actually allows the bark to form a little bit better on the bottom sides. Otherwise I honestly don't know if there's really much of a difference.
Smoke penetration; I can't tell any difference, but then again, the MAK has a good downdraft baffle system. If your pellet grill doesn't, then cooking on the top may make more of a difference.
Now if I want to catch the juices of something, then yes the top shelf with a pan underneath is the way to go.