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:
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.
An article about the pitfalls of using mice for animal research leads off with the example of calorie restriction. The controls for calorie restriction mice experiments were obese mice, suggesting that the health benefits of calorie restriction might be conflated with the health benefits of not being obese. I get the impression that people who study calorie restriction still think it worthwhile for life extension, but it's useful to try and integrate all evidence you come across.
[edit] timtyler suggests this is a well-understood effect that's already been taken into account by CR scientists.