@TrinidadLR4 see my post below about how to remove the factory plugs so you can install your roof rails. Should save you some time and possible damage to roof or glass;
Removing roof rail plugs
Regarding rails and boxes, I've always used a Skybox as well on my LR3 and LR4. I forget the specifics, but I think the extended rails give you one more forward setting for the crossbars, but I don't think you need it if memory serves. The LR3 factory rails were not extended forward. When I have a long box on my roof I like to have the crossbars as far apart as the mounts will allow. It kind of spreads out the load. I think we have all seen cars driving down the highway with long boxes wobbling forward and back because they are anchored by two points in the center. Anything that moves like that will wear, but my Skybox was always solid.
I haven't done a side by side comparison of the crossbar mounting locations on both racks and how that matches the max distance allowed by the Skybox clips, just giving my impression. The SkyBox is long, you may want it a bit more forward than back so it does not interfere with your rear lift glass.
Below is the only picture I could find of the SkyBox on my LR3. I think the lift glass would just barely make contact with the rear glass, but it still opened fine. If you buy the extended rails, the box will sit just forward of the lift glass and there will be no contact.
I think you are fine with either, though.