Just like cheaply built hardware is not in the same class has high quality built. When they opt to use a lower rated, cheaper made resistor in their circuitry it is indeed a lower quality part.
Then you have the engineering aspect. Volkswagen makes a CPU chip for their cars that adds 80 Horse Power. From just a chip. So, when you design a motherboard, what chipset do you use, how long are the pipes between everything, what material is it made of, can it handle more heat, do the pipes allow for more bandwidth?