The end result is that you need to use the cam profile or rocker ratios to compensate for head flow. If your heads flow less than 75% on the exhaust versus the intake then you need to compensate - i.e. Indy EZ1's from all the info I can find only flow 60% on the exhaust. A split pattern cam or a higher ratio exhaust rocker would be in order.

As for the "factory" analogy, that's just BS! The cars came off the line with enough power to get you in trouble and the engineers knew damn well that anyone wanting to improve things would have headers and a cam at the top of the list.