The crack and pop is the sound created when unburnt exhaust gases are ignited outside of the combustion chamber. The manifolds or headers get hot enough to ignite the unburned fuel that tends to build up during deceleration and this manifests itself as a pop or crack and if your exhaust was short enough, you would see the fire ball exiting the exhaust that go with this. A good visual of this happening on a regular basis would be NASCAR. When those care are off the throttle as they head into a corner, their short and non-muffled exhaust setups tend to create a constant flame thrower out the right side of the car. It's from all the unburned fuel getting ignited in their scorching hot headers. Your truck is the same way, just not nearly as dramatic.
Any free-flowing exhaust setup can create the cracks and pops you don't like. Straight-through muffler designs tend to make the cracking and poping more noticeable. Lack of cat-converters also magnifies the decel sounds too. Fortunately todays fuel injected vehicles are programmed to trim fuel on decel to help with MPG's and this helps prevent the decel noises. My setup is straight-through but it only pops a little bit if I let the rpms climb and decel for a long time. Under normal driving habits, mine never pops. If I had a manual trans that didn't alter the fuel delivery during decel, it would definitely pop like crazy. Lots of variables to this, but the origin of the decel noises is gas getting ignited in the exhaust system instead of in the engine combustion chambers.