The main issue is that a 6 cylinder motor with the same combined cylinder volume as a 4 cylinder motor has a lot more surface. So the ratio of surface to volume is higher in a 6 cylinder motor. The surface temperature is quite low compared to the temperature of burning fuel. Therefore, the more surface the motor has (or to be precise: the higher the surface to volume ratio is), the less efficient the fuel is burning, which gives you less power.
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