Landing Pads bolt on
g2d, I think what you're referring to is just the little cushy pieces that are used with a different, older Yakima system. My husband has black cushy foamy pieces that tend to fall off. These pieces sit between the tower and the bar. They are literally pads, not securing devices, which the Landing Pads are. After we remove his system, we have to re-set cradle tilt every time. It is a PITA, so no wonder people with this rack system tend to leave all the hardware on the vehicle all the time.
My Landing Pads and Towers are part of a newer system. The Pads bolt onto the topper's built-in tracks. They are not pads in the sense of cushioning; they are like hard footholds for the towers. (The COVER for the Landing Pads (only useable when the Towers and bars are removed) is a light plastic thing that clips on. I don't even bother putting those on, and the other vehicles I've seen with the same system also run around without the covers on the Landing Pads.)
My Towers lock directly into the Landing Pads. After initially setting up the bars and cradles for desired offset and tilt, there is no need to go through that fussiness again. To remove the crossbars, all I have to do is unlock the towers and lift each unit of bar-cradles-towers off as a fixed assembly. Then, when I want to pop them on again, I just put the tower feet into the Landing Pads and lock in place. Easy!