I just picked up my raptor yesterday so right now the cover is practically brand new. I ordered it with the factory tonneau cover, you can see the option on my sticker in my signature. After getting it, I didn't realize that it was a folding cover and not a roll-up. When I ordered it, the dealer didn't know. This won't work for the bed cage that I am going to be getting regardless if the bed cage was one to fit under a cover, I won't be able to get to the gas cans and tote box. So I am going to sell it.
I couldn't find a part number on it but I think it is this one.
Tonneau Cover - Soft Folding by Advantage, 5.5 Styleside Bed | The Official Site for Ford Custom Accessories
It does have the Ford logo on it.
Asking $300 plus shipping. PM me if interested.