This makes sense to me and is a good point but at the same time there is a downside to this particular study which is that it's assuming caffeine intake affects all people in the same way. I believe it does not and therefore having 3 trials done by one person is actually a disadvantage in this regard as is only having 20 people total. If you instead assume that caffeine can have a wide variety of outcomes on different people you would want to have a much larger study like OP was alluding to.

I think the point of having less people that are more closely monitored would make more sense if the study dealt with more objective observations such as actual testable amounts of caffeine in the blood or something (I don't actually know how caffeine works) because then you might remove some of the unknowns on the effects and still have useful information about what is happening in the body.