Complex sentence: They are intended to fill gaps that would otherwise hold air, not to create a layer between component and heatsink, because this would decrease the effectiveness of the heat transfer; ideally two perfectly smooth and flat metallic surfaces would not need heatsink compound.
Split into simpler sentences: They are intended to fill gaps that would otherwise hold air, not to create a layer between component and heatsink--this will decrease the effectiveness of the heatsink. Ideal perfectly smooth and flat metallic surfaces would not need heatsink compound.