If you plan to carry anything substantial up there, you might want to look into an aftermarket rack anyway. With the factory bars, width is limited to what fits between the side rails. Not long after getting my 4Runner, I removed the factory crossbars and went with Yakima Mighty Mounts and 54?" crossbars. After getting a feel for how the pieces work, install or removal of the Yakima rig takes maybe 5-10 minutes so installing as needed isn't too much of a chore.
I removed the rear rail caps using a metal cooking skewer (screwdrivers are too thick) to loosen the snap tabs. A diagram would have helped...I had to probe blindly and think I managed to break one tab, but the cap's still holding on after 4+ years. Even survived the dryer fans at an automatic car wash that somehow blew one of the rubber strips that sits in the channel below the side rails completely off the truck.
-Brent