I have existing Yakima Ridgeline towers (bases) and Jetstream bars from my CX-5, and am hoping that Yakima will either point to an existing base clip kit that works with the factor side rails or then manufactures a new one. Yakima recently updated their vehicle fit selection to include the CX-50, but it then asks someone local to them in Oregon to come in so they can figure out what clip kit will work. Here's hoping a CX-50 owner will do so soon.
But, I'm fairly confident that an existing clip kit should fit, given how many they already have. In fact, the outer clip that works on the CX-5 seems to also work on the CX-50 rail. But the CX-5 rail has backside holes unlike ours and the inside clip has a pin, plus the angles on that clip also don't seem to align well with the CX-50.