of you take a 4' level and put it across the corners, you will notice that your 2x4 upper rails are not 100% even, now when you go ahead and put your 3/4" plywood on top it will be the same, loads will always be on the highest point, no matter what. now if you had laid the 2x4 on the uprights, it would be 100% even, unless you had bowed 2x4's.
in your situation, since it's already built, what you can do is get a belt sander and even out the whole top, so you have no low spots. as far as skinning goes it has nothing to do with supporting weight, but to stiffen the stand against twisting and shifting.