In the 99 to 06 ext cabs the sub enclosures are usually straight back from the front of the box to the rear.
In the 07 to 13 ext cabs the sub enclosures are angled to fit over the rear of the ****** hump.
The 07 to 13 humbs are almost double in width at the very rear.
See here, the hump's height increases as well as its width.
See the inside of this box? That diagonal surface is to clear the hump.
Also see this for the bottom of the box.
Now, the 99 to 06 enclosures are not as bad. SOME companies make them the same, with a different front/vertical piece, as the newer models have a taller hump.
The hump height is about doubled in the 07 to 13s. But the fronts are about the same width.
Heres a 99 to 06 box.
Doesnt need to clear that big hump.