I think the basic issue is that many people don’t have a good mental model for floating-point comparisons. (This seems to be one of the eternal verities of floating-point arithmetic, not specific to Julia.) Once the issue is explained, objections to the atol=0 default almost invariably melt away.
It’s important to have this in Base for testing, and is also important because it is so easy to get wrong (especially in the array case, where you really want to use some norm of the whole array as a reference magnitude in most applications, but people’s first attempts almost always involve elementwise comparisons).