For example, maybe the Benzites require a gas that is poisonous to some other species?

They do, yes.

But I wonder if every species actually needs its own atmospheric mix? Maybe every species has its own ideal mixture of oxygen, nitrogen, CO2, etc.

I don’t think that they do, or if it does, it overlaps enough that it’s effectively a non-existent difference. They would be much more visibly impaired going planetside otherwise, since the ship wouldn’t be able to sustain it.