Yes, and here is the thing: you can't control for the total calories and vary only sugar intake. The change in sugar has to be offset by something else to keep the calories constant. So then to know whether a sugar change is responsible, we have to try different experiments with the same delta in sugar, but varying compensating substitutions.

I think you're missing the point.

It wouldn't make much sense to keep the groups isocaloric but replace the calories from sugar in one group with say, protein in another. You wouldn't be measuring the same thing any more.

The entire point of the study is comparing monosaccharides to polysaccharides and observing changes in 'health' (excuse the vague terminology). Sugar is substituted with a longer chain carbohydrate in well planned research.