What they are telling you is BS. What they do not want you doing is culturing your own because that means you are not purchasing so many of their products!
My experiences of culturing probiotics is that the amount of bacteria in a capsule is considerably lower than the amount in a yoghurt. It takes a very long time to culture the contents of a capsule, sometimes in the region of 16 hours at a suitable temperature of around 37C. Whereas my yoghurt can complete in around 3.5 hours.
Another possibility is that the bacteria are destroying one another whereas in the stomach they might find other food sources and be more separated from one another. They might not be compatible bacteria for culturing.