Get a copper rod. Place one end in ice water. Heat the other end with a blow torch. There will be a thermal gradient along the bar. Yes? One end will be very hot, one end will be cold. In the middle of the bar, the temperature will depend on the location along the length of the bar.

We have the exact same thing going on here.

Let's neglect all the thermal conductivity killing interfaces that are present between the core and the heatsink for the moment. Let's assume we have a perfect heat conduction path from the core to the air.

You have a heat source (the core)
You have a heat 'sucker upper' (the ambient air)

There WILL be a thermal gradient along the path from the core to the ambient air. The underside of the IHS will be hotter than the top side of the IHS. This is a fact of life.

I *think* you may be getting caught up by assuming a steady state (where everything is the same temperature) is reached. But it is not. Heat is always flowing from the source to the sink. As a result, there will always be a thermal gradient. As such, you are not measuring the core temperature when you measure the temperature of the IHS.