I would definately opt for the carpeted bed option with the rails installed on the floor and sides of the bed for future plans that change all too soon. The carpeting really keeps stuff from flying around back there, in addition to having the "D" rings on the rails for strapping stuff down with bungie cords.
I just keep my truck cover folded neatly but loosely in the bed area, and use it as a "bed" for any small to medium items to be carried. If you keep it "loose", it will hold just about any items in place.
I just couldn't see spending the ridiculous amount of money that the carpeted bed treatment costs.
I expect to get moisture in the bed with the rubber seal all around the cover and tailgate having to meet at corners. It's just too much to expect it to completely seal water-tight every time (especially when most admirers don't know to open the tailgate before closing the cover). Carpet might get and stay wet, if you're not careful. I love the retro look of the wood (like) rails that come with the bedliner option, though. I'm thinking of making some oak or walnut rails and adding them to my ABS bed. This wouldn't be very functional and I am not one to do a lot of customizing, but I think it would be great. I think I could always return it to stock, if I decide to later.
Funny thing...my tailgate has carpet even though the bed is not. Mine's not quite like the picture above. Hmmm.
The carpet on the tailgate was installed on all vehicles at the start of production due to quality problems with the base plastic cover. This is to change once the plastic item is corrected.
My SSR came with the tailgate carpet upgrade.
I did not get the carpet installed from the factory, mainly due to the moisture problem. I have installed a different type of carpet between the rails only. It looks like the tailgate carpet, but it can be removed should it get moisture in it.