One doesn't normally keep soil, with its rich microbial ecosystem, inside of their domestic toilet bowl.

One commonly puts something else with a rich microbial ecosystem in it on a regular basis.

Yes. However, it's "something else", meaning that the ecosystem is dramatically different. Furthermore, the majority of that ecosystem should be evacuated on a regular basis. E.g. bury an apple in soil during humid warm weather, and a week later it may be substantially decomposed; float it in a regular toilet bowl and it will recognizably still be an apple.