If the head is attached by 7/16" diameter head bolts, I still recommend 60-65 ft-lbs torque, regardless if the head is iron or aluminum, . While the Ft. Knox book suggests a 40 ft-lb setting for aluminum heads, the entire sentence reads "The head bolts are 3/8 inch in diameter and opposite bolts should be drawn up with a torque wrench to approximately 40 foot pounds." The 40 ft-lbs quoted is for 3/8" diameter bolts or, to be more precise, for the 3/8" diameter studs that were used on 1950 and earlier iron head 45 motors and which were used by the US Army prior to 1940.
As to cracking a head, personally I have never cracked a head, iron or aluminum, using the 65 ft-lb setting and a criss-cross torque pattern. As to pulling the threads from a bad hole, I'd rather the threads pull when I am rebuilding a motor than later when it is on the road. A heck of a lot easier to repair, although a pain, when you're in your shop with all of your tools. As it stands, if I am rebuilding a motor and the threads are visibly bad or questionable, I am going to repair the threads before the barrel is installed.
The real concern in torqueing heads is that all the bolts are drawn up evenly using a criss-cross pattern. The criss-cross pattern will prevent warpage of the head and improper stretching of the gasket. The proper torque will prevent a loose bolt or two from a causing a blow head gasket and/or a warped head. Aluminum heads warp more easily than do iron heads.