I was in a similar situation and I went to Fleet Farm and bought some strips of 1" wide, 1/4" thick aluminum and made braces to use in place of a rack. I then drilled / bolted the mounting plate from my top box to that. It was easy to do with just a drill and a hack saw and I ran that way for two years without issue.
I attached a pic of the two bars that I used to use on top of my current rack to give you an idea of what I made.