I'm no scientist, but I know certain things don't require digestion, at least not like other things. That's why the "Fit for Life, not Fat for Life" way of eating recommends you eat fruit until noon because fruit requires little or no digestive energy.
Again, I don't know the scientific answer, but after going on five MC's (I'm now on my 6th) I can testify that your digestive system definitely shuts down during the Master-Cleanse and you need to wake it up again when you start eating with orange juice and then soups, or you will suffer (again, I know from experience.)
I sense you are looking for scientific answers, but I'm not sure you will get them here.