There is a similar confound for intermittent fasting: if the IF animals lose weight, then that strongly implies that they were not doubling up on their feeding or whatever they needed to do to eat a normal amount of calories.

Some intermittent fasting studies have controlled for calorie intake, though. For example, this one:

Intermittent fasting dissociates beneficial effects of dietary restriction on glucose metabolism and neuronal resistance to injury from calorie intake.

It doesn't entirely rule out the possibility of reduced calorie intake being responsible - since consumed calories may not result is absorbed calories so reliably on intermittent fasting regimes. However, most explanations seem to focus on the more persistently lowered blood glucose levels and/or the increased stress.