True, but for a large scale operation you are going to want to have a bioreactor for both efficiency and scale, not to mention reducing the dead giveaway large quantity of people to tend the more manual methods.
Further complication include issues with production of the new substance possibly interfering with the lifecycle of the host itself. (That's the yeast if anyone didn't get that.) And let's not forget the separation and purification of the desired product.
You do know that they use microbes to make a number of different things, such as human insulin and interferon? Just look up some of the history of those developments, and you'll get a hint of some possible difficulties. Besides, there was a market for large quantities of cheap human insulin & interferon, while the previous methods of production were horribly inefficient and could never even come close to the demand.
I'm going to hazard a guess that the criminal cartels would be opposed to this technology because it would be more expensive to the them to set up, would require workers of a higher skill & training, would cut out entire chunks of their existing structure, and would be easily capable of flooding the market and suppressing prices.
Besides, other than banning the opiate producing strain, which only takes one leak to effectively neutralize that ban, what are you going to do? Ban genetically altered strains of microbes, and tobacco? Sorry, but I'd rather shoot the asshole that tries to do that, my life depends on one of those products, and so do a LOT of other peoples. Maybe you just want to ban the research into making illegal products. That would be a little better, but still futile. Eventually it will be easy enough to do that a talented high school student will someday succeed. Additionally, if it's not banned worldwide, someone will eventually do it someplace it's not illegal, and then there is the distinct possibility that it will get loose.
Of course, there is still something people are not looking at, their strain produces morphine, a controlled, but legal, substance. Yeah, it can be turned into heroin, but so can all the legal morphine which is usually made from FLOWERS that people grow! It's used in medicine. I was once in a hospital ward and I was the only patient not receiving morphine. (The reason for that doesn't matter.) So there IS a legal trade in the product produced by that yeast, but because it can be used to make an illegal one, some people want to ban it. You know, that's not a wise path to tread upon. If something can be banned because something illegal can be made from/with it, how long until everything is banned? You know politicians, give them an inch, and they'll run you over with your own vehicle and drag you a mile down the road.