Then what do you mean by:
It is standard practice - by those in the know - to use restricted animals as controls in CR experiments
One is comparing CR animals to non-CR animals. What do you mean by this?
I don't understand your question. "Proper" CR experiements use skinny experimental animals and skinny controls. Maybe 20% and 40% restricted - precisely to make sure that the control animals are not sick and obese.
Comparing with obese animals is bad - for all the reasons recently elaborated on - however this is really very old news in the community that are actually on such diets - and among most of the scientists involved.
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.