I picked up a used Sportrack box (Thule's lower end brand, made by Thule) in great shape for $80. My goals in having cross bars are to carry a cargo box and fork mounts (not simultaneously).
Since I don't have a pano roof, I wasn't concerned about the tight roof clearance, and I like the tight look of the flush cross bars. I recently installed NOS Whispbar flush aero bars to the factory rails on my GSW.