It seems as though some of the discussion assumes classical utilitarianism (or at least uses CU as a synecdoche for utilitarian theories as a whole?) But, as the authors themselves acknowledge, some utilitarian theories aren't hedonistic or totalist (or symmetrical, another unstated difference between CU and other utilitarian theories).
It is also a bit misleading to say that "many effective altruists are not utilitarians and care intrinsically about things besides welfare, such as rights, freedom, equality, personal virtue and more." On some theories, these things are components of welfare.
And it is not necessarily true that "Utilitarians would reason that if there are enough people whose headaches you can prevent, then the total wellbeing generated by preventing the headaches is greater than the total wellbeing of saving the life, so you are morally required to prevent the headaches." The increase in wellbeing from saving the life might be lexically superior to the increase in wellbeing from preventing the headache.
It would be interesting to survey responses to the sorts of interventions that provoke more negative responses (e.g., supporting the reduction of wild-animal habitats as a pro-WAW intervention, or a hypothetical "reprogramming predators" scenario––of course, the latter is very different insofar as it isn't currently technically feasible).