BOM doesnt include assembly costs, shipping costs, R&D costs, marketing costs. So BOM is good enough information for comparing 1st gen iPhone to the new 3G iPhone, it does not really tell you the actual money it costs apple to manufacture n sell one iPhone.
And they may not even be right, since they likely didn't have and iPhone 3G to take apart and look at.
Apple may or may not be using the same chipsets as others.
Something must have changed in the price, with the reduction in LCD costs, and memory -- Apple must have had a reason to cut costs in memory.
Or it might be that the 16GB didn't meet the battery life requirements yet.