It would appear based on what everyone else has said that the EXTERIOR dimensions of the bed are different. However the INTERIOR dimensions are the same. So as already said, the BedRug fits 04-11 same part#. Tonneau covers such as the BackFlip, Peragon, Solid Fold, etc that do not encapsulate the entire outer dimensions of the bed, are also interchangable from 04-11. However, solid fiberglass tonneaus that wrap the bed and caps certainly appear to be different part#s.
2013 Platinum EcoBoost SuperCrew
Ingot Silver 2WD 3.31
Boss Ultimate | ProComp | Toyo AT2's
Unleashed Custom Tuned
Peragon M3 PTM | BedRug