in fact it's a tentative to gain space in a 36 square base.
Stacking prisons seems a good idea.
My idea of prisons also increase the usefulness of prison whatever the missions of the month are: Supposed you have plenty of A Red Dawn mission with a level 2 prison you can stock 20, a chupacabra invasion (just an exemple, don't try to bring them all alive) you can still store 20, you don't have unused place.