I think the dust motes vs. torture makes sense if you imagine a person being bombarded with dust motes for 50 years. I could easily imagine a continuous stream of dust motes being as bad as torture (although possibly the lack of variation would make it far less effective than what a skilled torturer could do).

Based on that, Eliezer's belief is just that the same number of dust motes spread out among many people is just as bad as one person getting hit by all of them. Which I will admit is a bit harder to justify. One possible way to make the argument is to think in terms of rules utilitarianism, and imagine a world where a huge number of people got the choice, then compare one where they all choose the torture vs. one where they all choose the dust motes- the former outcome would clearly be better. I'm pretty sure there are cases where this could be important in government policy.