I remember reading that it's because they're impossible to do: the only option would be to lock people up in a room and only feed them exactly the same food on a schedule for months.
There is also the confounding factor of gut microbiome (people who had more fiber continuously IIRC having a more diverse/probably better for health, microbiome) influencing results of diet or vice versa.
Haven't they done nutrition studies in the military and in prisons because of the level of control over food intake?
Maybe, but how biased is the population? People in the army do a lot more physical exercise than most, people in jail have a different way of living than the rest of the population because of their circumstances.
Isn't that what control groups are for? Then you could rule out exercise or jail conditions as a factor.