However, look at the direction desktop hardware is going. Integration of more and more functionality into SoCs is the future for non-high performance desktop computing.

The more components that are integrated into the chip, the less there needs to be on the motherboard. Even better, all the high speed stuff can move onto the chip, making motherboard design easier. How long until SoCs come with RAM on die? Could you get away with a 4 layer motherboard in that case? So whilst you may lose economy of scale on the motherboard side, I think you will gain it back via integration, however, you will lose the ability to customise.