Now consider another hypothetical where people smoke cigarettes due to their biases, and other people without those biases have a significantly higher incidence of being run over by buses. Then, the biases that cause smoking cigarettes are not "significantly harmful on average" as compared to the alternative.

In addition to what others said (hypothetical examples are irrelevant for actual reality), it is not clear to what you compare the biases. What does "the same thought mechanism mean" in this case? Thought mechanisms don't have clear boundaries. If some pattern of thought is beneficial in some situations and harmful in others, we are free to call "bias" only its harmful applications.