Better breathing heads will improve the performance of an engine even if the intake is not upgraded at the same time.  There are already many out there with the Blue Thunder intakes on their Y’s so the heads will simply compliment their current combination but the new heads will still show an improvement with a stock intake in place.  You already see this in the circle track ranks where the stock intakes are required (many times with a two barrel carb in place) but head work or a better designed cylinder head is utilized to improve the engines performance.  The appropriate intake manifold will simply move the power bands around where the heads are more optimized.  This simply comes down to the sum of the parts making for a combination with different power attributes.  But most individuals opting for the new aluminum heads will very likely be using some form of aftermarket intake even if it's an older 3X2, 2X4, or one of the newer single four intakes.