I originally had a lot of yakima components from my VW GTI when i made the move to the new ex.
Swapped out the feet and such and mounted them on the explorer. After about 10k miles of messing with different sized fairings to stop the howl of the yakima bars i bought the ford ones and sold most of my yakima stuff.
Bars sat real high, about 2.5" above the rails. Wind noise was horrible, constant deep howl. I put on a yakima fairing, reduced some of the howling, but due to the moon roof, the edges of the fairing bounced on the steel roof, making a constant pinging noise. I modified the fairing, even cut one out of thicker gauge pvc and still had the issue. Due to the raised reinforcements of the roof, the feet from the fairing sit in the dwells, and the edges bounce on the peaks. Leaves a nice wear line mark in the clear coat too.
On top of all that, i lost about 3 mpg on the highway, consistently.
When i put the ford bars on, all the noise went away, mileage went back up, and i can still use my gear basket and ski rack.
A lot of the yakima stuff now comes in an "aero" model, designed specifically for factory bars.