Good question. 'They' tell you not to use it as fertilizer in your garden. 'They' tell you not to flush unused prescription drugs, as they have determined there are traces showing up in our tap water.
Anything that gets flushed goes through the sewage treatment plant, to be filtered and cleaned and returned to the water supply.
Pathogens and bacteria are not killed in composting for the garden. Due to a threat to human health, it is recommended to flush the poop where it will be treated by the treatment plants.
The main goal is to keep it out of natural waterways, where it not only is a threat to humans, but to our ecosystems.
So, flushing is the way to go...