I just received my 30". I asked Jeff the same question. To me it definitely would cause some back pressure having the water exit underwater. Will it make any measurable difference? I don't know. Jeff said it wouldn't make any measurable difference.
My sump water level is 8" and I think the exit is 7" I'm going to raise the skimmer an inch only because I'm obsessive - compulsive.
I don't think it will make a difference either way though.
Ken