I had a couple more thoughts to add...
If you yak has a rudder, it would be wise to put it stern forward on the vehicle so the wind won't bend your rudder while at highway speeds and running into the gusting winds. I have seen the results from having you rudder bent from the wind and it's not pretty.
I carry mine bottom down and supported by foam blocks underneath. A couple of carpet covered 2 X 2 added lengthwise under the kayak from rack to rack to support your kayak in the heat of the summer will reduce the oil can effect and folding effect. The material gets mighty soft in the sun on those 90+ degree days, not a big investment either. It also keeps it more steady from wagging back and forth in the wind.
The only disadvantage is if it rains and you have scupper plugs left in it or a Sit in kayak it will bend the kayak as it fills with water.