A big thing is storage. Apple uses extremely fast storage directly attached to the SoC and physically very very close. In contrast, most x86 systems use storage that's socketed (which adds physical signal runtime) and that goes via another chip (southbridge). That means, unlike Mac devices that can use storage as swap without much practical impact, x86 devices have a serious performance penalty.
Another part of the issue when it comes to cooling is that Apple is virtually the only laptop manufacturer that makes solid full aluminium frames, whereas most x86 laptops are made out of plastic and, for higher-end ones, magnesium alloy. That gives Apple the advantage of being able to use the entire frame to cool the laptop, allowing far more thermal input before saturation occurs and the fans have to activate.