It isn't an absolute comment, but rather a relative comment. Deficit is a relative word and I didn't want to be too verbose, but the implication here is that deficit refers to the relationship between your calorie consumption and your calories metabolized.
Set point weight theory does not disprove that consuming fewer calories than you burn will result in organic mass loss. There aren't exceptions to this fact as energy cannot be created from nothing.
Having a low set point means you have to endure more dramatic deficits to continue to lose weight sure but the basic math in calories remains the same. The remaining problems are psychological.
Well, this is not an absolute thing. If you reduce your calories your body can sense that, and will reduce your metabolism as well (e.g. reduce your average body temp or other body function). With the reduced metabolism you will probably still keep your original mass. And then we didn't even talk about carb-protein difference, while those still has the same calorie content, their metabolic effect is totally different.
Search for "set point weight theory" for more info.