The extra heat in this case is the different amounts transfered proportionately to the air.
The average molecular energy state (i.e. temperature) of the air will increase in a closed environment because more of it is transfered via the HSF, compared to the poorer HSF where the average molecular energy state of the cpu materials is relatively higher.
And example
If the thermal load (say 50W) is the same for both:
1. A quality HSF may transfer 80% of that into the atmosphere. So 40W of energy is now transfered to the air via the HSF.
2. A poorer HSF using the same 50W of waste heat, can only transfer 60% of the heat into the air, meaning the cpu will be hotter. Right?
Based on the above logic, the same energy load is available in each case, but different HSF efficiencies mean that a different percentage of energy can be transfered.
This would seem to me to explain how the temperature would increase, and is the principle reason why case air flow is so important. Am i missing something?