MB on horde are better at capping alliance towers while MB on alliance are better at defending alliance towers. It's pretty difficult to get 5 toons up the winding staircase in towers that alliance is supposed to attack, whereas it's relatively easy to get 5 toons up the towers that horde is supposed to attack. So, if I was to play horde, I would be offensively capping towers ahead of the Balinda mob. Since I play alliance, i go back and recap the towers that horde captured thereby delaying them and often causing our side to win (if we have a tank that is).

To sum up, as a multiboxer you do most of your tower fighting in alliance towers... whether you're attacking them or defending them.