Nobody has mentioned the obvious......
Well, obvious to me.
Alum has faaaar less strength than iron/steel. The deck thickness of E heads is going to be about 5/8" thick. The deck thickness on iron heads is probably about 3/8". Similarly, the columns around the head bolt holes, port wall thickness, etc. Guess where this extra thickness comes from.....
intrusion into the coolant space so that the alum heads have less coolant volume in them.
I believe a better water pump &/or smaller pump pulley would likely fix the problem.
It should be tried.