To be honest I don't cover my dirt at all. I make sure it's natural soil with no fertilizers or perlite or anything else non-dirt, but I leave it at that. I feel like animals have evolved with and around dirt and other organic debris since the dawn of time, I think they know how to handle themselves with it. It is loose, particulate matter after all. A well hydrated animal shouldn't, IN THEORY have problems with a little of it. My dog has certainly swallowed mouthfuls of it throughout her life and she's still here to tell the tale. The puppy that eats the socks, on the other hand... certainly poses a problem! And we trust females with a bin full of sand or soil in the cage full-time, but then cover the plant pots. It's never made too much sense to me.
It certainly may hold something, since a variety of animals will eat dirt or clay to get something they are missing as far as minerals. Mine don't eat it that I know of, but they do get a lot of feeder variety and I gutload well, so that may be a reason. We have to remember that not all animals are built the same way, so while one supplement may work really well for 100 chameleons, for 1 with a slightly different system it may not be enough/adequate and they feel the need to supplement themselves however they can. That's why the diet of chameleons seems to be such an art lol There's so much to consider and put together in a way that works for each animal you own.