I'm no expert and I'm sure some of the senior members will soon chime in but I recently pondered this as well. I found this sentence from Chameleon e-zine "The reason for avoiding Perlite is that these plants would be used in cages with babies and/or adult chameleons. I have noticed chameleons have a taste, so to speak, for perlite. If ingested in large amounts it could cause an impaction. This would be even more of a problem with smaller chameleons. Even when you cover the soil with large river rock to keep the chameleons out, they will try and shoot their tongues through the rocks to get to the prelite.". They do talk about using Perlite for incubating eggs though. I've heard hydroton is the best for drainage.
Of course thier are so many layers of substrate I don't really understand how a chammy would accidently eat the drainage layer, I used Perlite before I read that article but my layer is about 3 inches down and I dont see my pygmy digging all that way to eat it.