The difference is that in soviets (in the original sense) the workers held actual power. Bayer still wants full control over their workers, they just want to offload all the responsibility normally held by middle management to them as well.

They're trying to get rid of "hierarchies" without getting rid of the power structure. I don't see how this benefits the workers at all.

No, because self-organizing does not imply ownership of the means of production.