Yes, I believe that it is only a moisture issue. Since it is not a complete seal (holes for levers & wires & such) it is not intended to be a hermetic seal to keep out any gasses such as CO or CO2. Those are taken care of in the basic design of the car (i.e., the exhaust is at the rear where it is directed away from the passenger cabin by the air flow around the car). That's why safety inspections are typically very critical of after market exhausts, particularly side exhausts.

I can't remember who mentioned it earlier in your thread but there are indeed holes at the bottom of the door to let water flow out. There's no way that you'll ever be able to keep water out so the best approach is to let any accumulated water out. If the VB is missing, moisture can damage the door panel, speakers & wires. If those holes ever get clogged, enough water can accumulate in the door to actually slosh around and spill into the cabin (sounds silly but it actually happened on my TLC). As JAMAS mentioned, a lot more water goes through that door than you would ever expect.