I tried posting the issues in a couple of the entomology forums I belong to, but most responses were not to even use the dome, but "Riker mounts", which are like a shadow box frame except the Riker has a good seal built in, and then to lock them in a drawer somewhere.
People that have domes often just glue the glass to base and place nothing inside either to deter pests or moisture. They count on the seal to do the job of keeping the pests out. I'm probably going to have to go this route except I'm going to keep active silica gel inside to keep humidity minimal. As for the moth flakes, I'm just going to have to remove them. The insects were all toaster oven dried for at least a week, and then placed into a sealed container with a lot of silica gel for at least a month. I feel quite confident there won't be any mold issues and there shouldn't be pests either as long as the silicone seal is intact.