I have the Bakflip G2 installed on my truck. My bed extender will barely clear. Another member on here (Mhannis I think) had mentioned that he had to grind a little off either the top of the extender bracket or bottom of the G2's rail clamps. I plan to grind off a little eventually since it seems to rub a little when I slide it forward. During install make sure you mount the center clamp as high up as possible to help with the clearance. Some members also reported that they did not install the center clamps and had no issues. There are several threads here that helped me with my decision.
I have a G2 cover also. I do not have the bed extender, but I do have a bed divider. It slides without any issues and clears the cover and brackets without any issues.