Well mulch is not coco dirt or soil but it is substrate.Are you positive that is why the chameleon died? I know you aren't going to be able to prove that since it was in the past so don't worry about it unless you can provided proof other than a chameleon died in pet store eating cricket then later died .
The breeding for bacteria? What is a dirty chameleon cage with paper towels or even bare bottom? They are all breeding grounds for bacteria if not maintained.
My point is, I do use bare bottoms in most chameleon screen cages, but I have also used a lot of substrates mainly coco or soil in some bottom trays and terrarium. Yes I think its not for your typical chameleon owner since you have to make sure not to over water ect. I just want to see if anyone can prove the harm since it is such a forum standard and nobody even knows why.