It depends on what you're trying to figure out. If you're trying to figure out just the effects of location (which pretty much means zero G and extra radiation) then you're right, you need to control all the other factors. (You could even isolate the zero G effects by subjecting the control subject to extra radiation, though that might not fly with the ethics boards.) But if you're trying to figure out the sum total effects of space flight, including all the ancillary effects (like decreased social interaction) then it makes sense to let the control subject just live a normal life.