Well let us see if I can be completely wrong about something.
Let's say each sub requires 1 cu/ft of space(just a number I threw out), if you partition them, basically two separate boxes you need to make it 2 cu/ft, but if the subs share the same air space they see 1/3 of the other subs air space. Not really explaining it all that well. But for the 2 in the common box you would only need 1 1/3 cu/ft, so if space was a factor it could help having them share the air space.