I know one reason is because of the torque difference between the manifolds. The iron intakes can torque a lot higher. Aluminum intakes are only supposed to get like 20 LB FT. I'm sure that's not the only reason. I ran into the same thing on the 351M in my truck. It has a factory intake valley, but with the aluminum intake I have to stack gaskets on top and bottom of the intake pan. Why? "That's just how it is" is the best answer I know. lol