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From 99-2016 the beds interior really didn't change. I have a Pace Edwards metal retractable from a 2000 on my 2014 and it is fine. The tailgate changed in 2008 (tailgates with the Ford in the middle of the gate) so the top of the gate changed so the fitment of any cover that would come over the top of the gate might not fit.
Anything that touches the inside of the gate or touches the top should be ok. There was a guy who modded his back window of the cap to work with the newer style gate too, so if you can mod it you may be ok.
I just sold my Leer and went to the dealer to get the model # and fitment guide so I could post the info with it. Mine was a 06 long bed. It would only fit 99-08 Super Dutys only. It was a hard flat tonneau that fit over the exterior edge of the bed.
When I upgrade my gate to the '08 style the weather strip on my cap that overlaps the outside edge of the gate doesn't sit right. The '08+ gates have a different edge profile than earlier gates so the hatch is where there may be an issue. In my case pushing the cap back about 1/2" allowed the seal to lay flat enough to look ok, but that will vary depending on the style of cap.