for one, you can keep both ports butted into the corners. you can also have the walls as close to the subs as possible. both of these help with spl.Why would you use 2 3cuft boxes boxes instead of 1 6cuft box? whats the advantage to 2 subs per box instead of 4 in 1 big box?
you can also find a gain by having 1 box further back than the other, off setting them on an angle, or having some space in between the 2 boxes.
2 boxes are much more versatile, especially when the end goal is spl.