The oval holes make more sense if you think about the difference between the aftermarket rack designs and the factory roof rails. Most aftermarked designs are a pair of side to side cross bars, one fore and one aft. But the factory rails which are permanently installed are longer rails running front to back, one on each side. The oval holes make sense for these long rails if you take into account differential heating and cooling. The roof panels and the rails will expand and contract at different rates if they are different materials.So the rails will effectively be getting longer or shorter in relation to the roof panel they are mounted to. If you don't allow for that slight movement with oval mounting holes, the metal roof will buckle or stretch, or the rails will. You see the oval hole fix used a lot in woodworking where moisture and grain differences produce relative movement that would split the wood.
It's less of a risk with the side to side aftermarket rails since the bow of the roof provides plenty of room to flex. It's the extra length and stiffness where the factory rails mount just above the strong door frames that would likely cause a problem. Of course, this is all just a guess on my part.