I think it's advised not to have substrate in a non-bio enclosure for sanitary purposes, mainly. A spongey substrate like coco coir with no beneficial organisms is just a bacteria catcher.
Chunky soil with easily-ingestible, but not passable pieces are always an impaction risk (bio or not) with chameleons, who can easily miss a target or pick up a piece of something with it.
A bioactive enclosure should have the substrate covered by leaf litter. Leaves aren't easy to suck down with a bug, even if a chameleon accidentally grabs one.
I suppose if you were dead set on substrate in a non-bio enclosure, you could cover it with leaf litter. But it'd just make cleaning that much harder, and you'd still end up having to replace it all every so often.