I think you guys are dismissing Kevin's comments a little too quickly. While air is "stuff," it will not show the effects of radiant heating as measured with a thermometer probe. Heating the air occurs to some extent from radiant energy but it's mostly convection. That's the way your radiator in your home heats the room. Since it is hotter than its surroundings, there is a bit of radiant heating that occurs but the surface of the radiator itself does not get hot enough to contribute significant heating through radiation. The name "radiator" is somewhat of a misnomer in this case.
To illustrate the effect of radiant heat transfer as opposed to convection alone, think about the temperature difference between air and anything that's been lying out in the sun on a bright afternoon like an asphalt surface or your car. The asphalt surface can easily be 40 or 50 degrees hotter than the ambient temperature due to the way it absorbs radiant heat energy.
In the case of the WSM and clay pot base, the base becomes a source of radiant energy only after it's been heated by the fire. At that point, a piece of meat on the bottom rack is definately going to recieve more energy than one on the top rack. This is due to the fact that radiant energy's intensity lessens with distance from the source (and by the fact that the meat on the bottom rack is blocking that energy's path to the top grate). Think about how warm you get standing next to a fire. Does the air get as hot as your face? No. As you back away from the fire, this effect decreases dramatically because the radiant energy is becoming more diffuse.
The reason that radiant heat is not an issue with a pan full of water is because the temperature of that water never gets above 212 degrees. Once it rises beyond 212, it becomes a gas and it, along with it's heat energy, is distributed by convective means throughout the cooker.
In conclusion, it is very possible that due to convective currents within the cooker, that temperatures measured by a thermometer probe could be equal thoughout the cooking chamber, but the meat closest to a source of radiant heat is still going to cook faster. This has already been proven by those of us that have used sand in the pan.
Now, the important question that is raised is whether or not the base is a source of radiant and if so, does it radiate enough heat to alter cooking times? If the surface of the base gets as hot as the surface of a pan full of sand, then the answer is yes.
More food for thought: how would wrapping the base in foil affect it as a radiant heat source? If you wrap the bottom of the pan, radiant energy from the fire is reflected away from the pan back toward the bottom of the cooker. The base will not radiate as much heat from its surface if you do this. So what if you foil the top of the base? Well, the radiant heat from the surface of the base will travel across the air gaps between the base and the foil and it will stop right there. Some may be reintroduced into the cooking chamber by radiating off the surface of the foil but it's intensity will be diminished.
So where does this leave us? The easiest way to determine what's going on would be to cook similar pieces of meat, one on the top rack and one on the bottom, without flipping and look at the results. I have yet to do this but I would suspect that the surface of the meat on the bottom rack facing the base would be significantly more cooked and possibly drier than them top suface of the meat on the top rack. It would then be useful to try it foiled to see how much that helps diffuse the radiant heat and negate the effects we've been discussing.