in the summer I run a full length rack, winter a Yakima space booster ( for skis etc) without the full rack. Only issue I saw early on was if you mount it to the stock rack with the recommended spacing then you can not fully open your tailgate..as the space box sat too far back.
however, for me, I have extra length rails and an extra crossbar that I made up for my full length rack. regardless..
.that would be my question for a box on standard rails and one of the posts above looks like their box sits back and would interfere with the tailgate